Empirical PE reference assembly tutorial
This tutorial demonstrates a reference-based assembly for an empirical 2RAD dataset in ipyrad2 with additional WGS samples included. All reads are paired-end 2 x 150bp in length. The RAD dataset was prepared using the 3RAD protocol.
Download the data
The data in this tutorial are not yet publicly available.
Assembly
trim RAD data
The data are already demultiplexed to individual samples, so we can start by running read trimming. Here we
will run trim twice, first on the RAD-seq samples, and then on the WGS samples. This is will allow the
trim method to detect and remove the restriction motif from the beginning of each RAD-seq read. These
patterns are not present on the WGS sequences, so we will run trimming on the RAD and WGS samples separately.
Here we use -d to specify input fastq paths, and -o to specify output directory paths, and also specify
the number of cores available (-c) and how to distribute these resources among multi-threaded jobs (-t).
The logging report shows that it detected 19 paired samples from our input data paths, and that these samples consistely start with the restriction cutsite motifs "ATCGG" on R1s and "TAGCTT" on R2s. It reports the progress of the run until completed, and then prints the path to the output fastqs and stats file.
ipyrad2 trim \
-d TUTORIAL/FASTQS/RAD/*.fastq.gz \
-o TUTORIAL/TRIM/RAD/ \
-c 12 -t 4
ipyrad2 trim rad log
2026-07-22 15:28:04 | INFO | cli_main.py | ----------------------------------------------------------
2026-07-22 15:28:04 | INFO | cli_main.py | ----- ipyrad2 trim: quality, adapter, and cutsite motif trimming -----
2026-07-22 15:28:04 | INFO | cli_main.py | ----------------------------------------------------------
2026-07-22 15:28:04 | INFO | cli_main.py | CMD: ipyrad2 trim -d TUTORIAL/FASTQS/RAD/SLH_AL_0012_R1.fastq.gz TUTORIAL/FASTQS/RAD/SLH_AL_0012_R2.fastq.gz TUTORIAL/FASTQS/RAD/SLH_AL_0013_R1.fastq.gz TUTORIAL/FASTQS/RAD/SLH_AL_0013_R2.fastq.gz TUTORIAL/FASTQS/RAD/SLH_AL_0014_R1.fastq.gz ...[truncated; 38 total matched paths] -o TUTORIAL/TRIM/RAD/ -c 8 -t 4 -f
2026-07-22 15:28:04 | INFO | names.py | paired files by auto-detecting mate tokens in filenames
2026-07-22 15:28:04 | INFO | names.py | showing first 10/19 names parsed from file paths
2026-07-22 15:28:04 | INFO | names.py | SLH_AL_0012 <- ('SLH_AL_0012_R1.fastq.gz', 'SLH_AL_0012_R2.fastq.gz')
2026-07-22 15:28:04 | INFO | names.py | SLH_AL_0013 <- ('SLH_AL_0013_R1.fastq.gz', 'SLH_AL_0013_R2.fastq.gz')
2026-07-22 15:28:04 | INFO | names.py | SLH_AL_0014 <- ('SLH_AL_0014_R1.fastq.gz', 'SLH_AL_0014_R2.fastq.gz')
2026-07-22 15:28:04 | INFO | names.py | SLH_AL_0018 <- ('SLH_AL_0018_R1.fastq.gz', 'SLH_AL_0018_R2.fastq.gz')
2026-07-22 15:28:04 | INFO | names.py | SLH_AL_0030 <- ('SLH_AL_0030_R1.fastq.gz', 'SLH_AL_0030_R2.fastq.gz')
2026-07-22 15:28:04 | INFO | names.py | SLH_AL_0034 <- ('SLH_AL_0034_R1.fastq.gz', 'SLH_AL_0034_R2.fastq.gz')
2026-07-22 15:28:04 | INFO | names.py | SLH_AL_0036 <- ('SLH_AL_0036_R1.fastq.gz', 'SLH_AL_0036_R2.fastq.gz')
2026-07-22 15:28:04 | INFO | names.py | SLH_AL_0042 <- ('SLH_AL_0042_R1.fastq.gz', 'SLH_AL_0042_R2.fastq.gz')
2026-07-22 15:28:04 | INFO | names.py | SLH_AL_0048 <- ('SLH_AL_0048_R1.fastq.gz', 'SLH_AL_0048_R2.fastq.gz')
2026-07-22 15:28:04 | INFO | names.py | SLH_AL_0063 <- ('SLH_AL_0063_R1.fastq.gz', 'SLH_AL_0063_R2.fastq.gz')
2026-07-22 15:28:04 | INFO | trim_fastqs.py | trim input preflight found 19 usable samples and 0 skipped empty samples
[####################] 100% | Counting kmers - total jobs: 19
[####################] 100% | Counting kmers - total jobs: 19
2026-07-22 15:28:08 | INFO | trim_fastqs.py | cutsite motifs set to R1=[ATCGG] at offset 0 R2=[TAGCTT] at offset 0
2026-07-22 15:28:08 | INFO | trim_fastqs.py | trimming/filtering 19 samples with 'fastp' and writing to /home/deren/Documents/ipyrad-tests/TUTORIAL/TRIM
2026-07-22 15:28:08 | INFO | trim_fastqs.py | running up to 2 parallel jobs each using up to 4 threads
[####################] 100% | Trimming - total jobs: 19
2026-07-22 15:38:26 | INFO | trim_fastqs.py | trimming stats written to /home/deren/Documents/ipyrad-tests/TUTORIAL/TRIM/RADipyrad_trim_stats_0.txt and /home/deren/Documents/ipyrad-tests/TUTORIAL/TRIM/RAD/ipyrad_trim_stats_0.json
The stats file report shows the following. There are ~500K read pairs per sample. The proportion of bases with quality scores >20 or >30 increases slightly after trimming. About ~20K reads were filtered from each sample, and ~100K bases were trimmed from each sample.
cat TUTORIAL/TRIM/RAD/ipyrad_trim_stats_0.txt
CMD: ipyrad2 trim -d TUTORIAL/FASTQS/RAD/SLH_AL_0012_R1.fastq.gz TUTORIAL/FASTQS/RAD/SLH_AL_0012_R2.fastq.gz TUTORIAL/FASTQS/RAD/SLH_AL_0013_R1.fastq.gz TUTORIAL/FASTQS/RAD/SLH_AL_0013_R2.fastq.gz TUTORIAL/FASTQS/RAD/SLH_AL_0014_R1.fastq.gz ...[truncated; 38 total matched paths] -o TUTORIAL/TRIM/RAD/ -c 8 -t 4 -f
total_reads_before total_bases_before q20_rate_before q30_rate_before read1_mean_length_before read2_mean_length_before total_reads_after total_bases_after q20_rate_after q30_rate_after read1_mean_length_after read2_mean_length_after reads_filtered_by_low_quality reads_filtered_by_too_many_N reads_filtered_by_low_complexity reads_filtered_by_too_short adapter_trimmed_reads adapter_trimmed_bases
SLH_AL_0012 563176 80001289 0.954069 0.911111 141 142 497944 66873966 0.981349 0.948682 134 134 63800 32 2 1398 16966 105734
SLH_AL_0013 146094 20281405 0.954693 0.910566 139 138 129446 16969956 0.981259 0.947499 132 129 16214 10 2 422 8521 61117
SLH_AL_0014 443004 61969524 0.956256 0.912269 139 140 395550 52340611 0.983580 0.950033 132 132 46132 52 4 1266 14011 100130
SLH_AL_0018 399974 56367849 0.955489 0.912426 141 140 354654 47231153 0.981967 0.949155 134 131 44304 34 4 978 12822 82471
SLH_AL_0030 549442 77490308 0.949871 0.904072 140 141 479712 63927960 0.979807 0.945329 133 133 68412 62 16 1240 16358 106977
SLH_AL_0034 919528 129257044 0.957052 0.913076 139 141 824964 109686676 0.983515 0.949865 132 133 92498 86 6 1974 25575 172774
SLH_AL_0036 560770 79099258 0.956150 0.912363 139 142 501304 66891797 0.983463 0.950077 132 134 58250 66 16 1134 16225 105836
SLH_AL_0042 541960 76126373 0.948882 0.902434 140 140 471154 62526059 0.979608 0.944598 133 132 69448 44 6 1308 16587 115752
SLH_AL_0048 381132 53734169 0.956733 0.913493 139 142 341132 45510921 0.983839 0.950918 132 134 39024 44 2 930 11480 73544
SLH_AL_0063 322578 45163232 0.956649 0.915023 141 138 287666 38081673 0.981918 0.949984 133 130 33886 34 0 992 13174 96015
SLH_AL_0064 706128 100558899 0.952658 0.908034 142 142 619146 83410659 0.980672 0.947017 135 134 85520 62 2 1398 21361 114197
SLH_AL_0084 249296 35235114 0.956800 0.914646 140 141 221634 29619760 0.982823 0.950826 133 133 26972 30 2 658 11371 66049
SLH_AL_0100 630198 88883272 0.951891 0.907221 142 139 553546 73808801 0.980239 0.946311 135 131 75416 74 2 1160 17966 118649
SLH_AL_0101 894498 127625723 0.950925 0.905928 142 142 782744 105652472 0.980218 0.946168 135 134 110264 70 2 1418 21758 111997
SLH_AL_0104 728720 103161918 0.952420 0.908515 140 142 641002 85810622 0.980896 0.947689 133 134 86212 78 8 1420 21701 137332
SLH_AL_0105 529698 73862769 0.958234 0.915753 139 139 476570 62883408 0.983888 0.951379 132 131 51740 52 8 1328 16232 126928
SLH_AL_0106 676214 96331896 0.953310 0.909506 142 142 594574 80161167 0.980783 0.947751 135 134 80058 64 2 1516 20532 115082
SLH_AL_3065 200288 28146435 0.953608 0.910337 139 141 176412 23447184 0.981538 0.948949 132 133 23316 10 4 546 10433 64039
SLH_AL_3066 461010 65195993 0.956640 0.914975 141 141 411400 55046995 0.981874 0.949931 134 133 48518 36 0 1056 14140 93647
trim WGS data
Next we run trim on the WGS samples. You can skip this step if you do not wish to add any
WGS samples. Because these samples contain many more reads they take a bit longer to run.
To improve runtimes, and normalize inputs among samples, you can optionally use the
-x/--max-reads flag here to keep only the first N number of reads from any sample.
ipyrad2 trim \
-d TUTORIAL/FASTQS/WGS/*.fastq.gz \
-o TUTORIAL/TRIM/WGS/ \
-x 5_000_000 \
-E \
-c 12 -t 4
ipyrad2 trim wgs log
2026-07-22 18:38:59 | INFO | cli_main.py | ----------------------------------------------------------
2026-07-22 18:38:59 | INFO | cli_main.py | ----- ipyrad2 trim: quality, adapter, and cutsite motif trimming -----
2026-07-22 18:38:59 | INFO | cli_main.py | ----------------------------------------------------------
2026-07-22 18:38:59 | INFO | cli_main.py | CMD: ipyrad2 trim -d TUTORIAL/FASTQS/WGS/21040XD-01-07_S39_L002_R1_001.fastq.gz TUTORIAL/FASTQS/WGS/21040XD-01-07_S39_L002_R2_001.fastq.gz TUTORIAL/FASTQS/WGS/21040XD-01-08_S40_L002_R1_001.fastq.gz TUTORIAL/FASTQS/WGS/21040XD-01-08_S40_L002_R2_001.fastq.gz ...[truncated; 8 total matched paths] -o TUTORIAL/TRIM/WGS/ -x 5_000_000 -E -c 12 -t 4
2026-07-22 18:38:59 | INFO | names.py | paired files by auto-detecting mate tokens in filenames
2026-07-22 18:38:59 | INFO | names.py | showing first 4/4 names parsed from file paths
2026-07-22 18:38:59 | INFO | names.py | 21040XD-01-07_S39_L002 <- ('21040XD-01-07_S39_L002_R1_001.fastq.gz', '21040XD-01-07_S39_L002_R2_001.fastq.gz')
2026-07-22 18:38:59 | INFO | names.py | 21040XD-01-08_S40_L002 <- ('21040XD-01-08_S40_L002_R1_001.fastq.gz', '21040XD-01-08_S40_L002_R2_001.fastq.gz')
2026-07-22 18:38:59 | INFO | names.py | 21040XD-01-09_S41_L002 <- ('21040XD-01-09_S41_L002_R1_001.fastq.gz', '21040XD-01-09_S41_L002_R2_001.fastq.gz')
2026-07-22 18:38:59 | INFO | names.py | SRR15412865 <- ('SRR15412865_1.fastq.gz', 'SRR15412865_2.fastq.gz')
2026-07-22 18:38:59 | INFO | trim_fastqs.py | trim input preflight found 4 usable samples and 0 skipped empty samples
2026-07-22 18:38:59 | INFO | trim_fastqs.py | cutsite motifs set to R1=[<none>] at offset 0 R2=[<none>] at offset 0
2026-07-22 18:38:59 | INFO | trim_fastqs.py | trimming/filtering 4 samples with 'fastp' and writing to /home/deren/Documents/ipyrad-tests/TUTORIAL/TRIM/WGS
2026-07-22 18:38:59 | INFO | trim_fastqs.py | running up to 3 parallel jobs each using up to 4 threads
[####################] 100% | Trimming - total jobs: 4
2026-07-22 18:54:09 | INFO | trim_fastqs.py | trimming stats written to /home/deren/Documents/ipyrad-tests/TUTORIAL/TRIM/WGS/ipyrad_trim_stats_0.txt and /home/deren/Documents/ipyrad-tests/TUTORIAL/TRIM/WGS/ipyrad_trim_stats_0.json
The stats report shows a slightly higher adapter contamination in this dataset, with one sample trimming adapters in nearly 10% of reads. The base quality is lower in the one sample with 300 bp reads than in the other samples with 150 bp reads, reflecting differences in the technologies used to sequence these samples.
cat TUTORIAL/TRIM/WGS/ipyrad_trim_stats_0.txt
CMD: ipyrad2 trim -d TUTORIAL/FASTQS/WGS/21040XD-01-07_S39_L002_R1_001.fastq.gz TUTORIAL/FASTQS/WGS/21040XD-01-07_S39_L002_R2_001.fastq.gz TUTORIAL/FASTQS/WGS/21040XD-01-08_S40_L002_R1_001.fastq.gz TUTORIAL/FASTQS/WGS/21040XD-01-08_S40_L002_R2_001.fastq.gz ...[truncated; 8 total matched paths] -o TUTORIAL/TRIM/WGS/ -x 5_000_000 -E -c 12 -t 4
total_reads_before total_bases_before q20_rate_before q30_rate_before read1_mean_length_before read2_mean_length_before total_reads_after total_bases_after q20_rate_after q30_rate_after read1_mean_length_after read2_mean_length_after reads_filtered_by_low_quality reads_filtered_by_too_many_N reads_filtered_by_low_complexity reads_filtered_by_too_short adapter_trimmed_reads adapter_trimmed_bases
21040XD-01-07_S39_L002 10000000 1510000000 0.961961 0.917460 151 151 8718158 1298721695 0.987971 0.962181 149 148 1248882 26 398 32536 370126 7662366
21040XD-01-08_S40_L002 10000000 1510000000 0.969503 0.931227 151 151 9090450 1334383169 0.989339 0.965528 147 146 842934 10 476 66130 1116069 31804344
21040XD-01-09_S41_L002 10000000 1510000000 0.960757 0.916889 151 151 8805934 1304337361 0.987865 0.962097 148 147 1067662 22 246 126136 505151 21563173
SRR15412865 10000000 2494480397 0.936768 0.896631 249 249 8258378 2020158740 0.981638 0.967588 246 242 1721446 818 398 18960 15326 1531004
map RAD data
Next map the trimmed RAD fastqs to the reference genome.
ipyrad2 map \
-d TUTORIAL/TRIM/RAD/*.fastq.gz \
-r TUTORIAL/REFERENCE/AmaTu_v01_no00_renamed.fa \
-o TUTORIAL/MAP/RAD/ \
-c 12 -t 4
ipyrad2 map rad log
2026-07-22 17:17:26 | INFO | cli_main.py | CMD: ipyrad2 map -d TUTORIAL/TRIM/RAD/SLH_AL_0012.R1.trimmed.fastq.gz TUTORIAL/TRIM/RAD/SLH_AL_0012.R2.trimmed.fastq.gz TUTORIAL/TRIM/RAD/SLH_AL_0013.R1.trimmed.fastq.gz TUTORIAL/TRIM/RAD/SLH_AL_0013.R2.trimmed.fastq.gz ...[truncated; 38 total matched paths] -r TUTORIAL/REFERENCE/AmaTu_v01_no00_renamed.fa -o TUTORIAL/MAP/RAD/ -c 8 -t 4 -f
2026-07-22 17:17:26 | INFO | names.py | paired files by auto-detecting mate tokens in filenames
2026-07-22 17:17:26 | INFO | names.py | showing first 10/19 names parsed from file paths
2026-07-22 17:17:26 | INFO | names.py | SLH_AL_0012 <- ('SLH_AL_0012.R1.trimmed.fastq.gz', 'SLH_AL_0012.R2.trimmed.fastq.gz')
2026-07-22 17:17:26 | INFO | names.py | SLH_AL_0013 <- ('SLH_AL_0013.R1.trimmed.fastq.gz', 'SLH_AL_0013.R2.trimmed.fastq.gz')
2026-07-22 17:17:26 | INFO | names.py | SLH_AL_0014 <- ('SLH_AL_0014.R1.trimmed.fastq.gz', 'SLH_AL_0014.R2.trimmed.fastq.gz')
2026-07-22 17:17:26 | INFO | names.py | SLH_AL_0018 <- ('SLH_AL_0018.R1.trimmed.fastq.gz', 'SLH_AL_0018.R2.trimmed.fastq.gz')
2026-07-22 17:17:26 | INFO | names.py | SLH_AL_0030 <- ('SLH_AL_0030.R1.trimmed.fastq.gz', 'SLH_AL_0030.R2.trimmed.fastq.gz')
2026-07-22 17:17:26 | INFO | names.py | SLH_AL_0034 <- ('SLH_AL_0034.R1.trimmed.fastq.gz', 'SLH_AL_0034.R2.trimmed.fastq.gz')
2026-07-22 17:17:26 | INFO | names.py | SLH_AL_0036 <- ('SLH_AL_0036.R1.trimmed.fastq.gz', 'SLH_AL_0036.R2.trimmed.fastq.gz')
2026-07-22 17:17:26 | INFO | names.py | SLH_AL_0042 <- ('SLH_AL_0042.R1.trimmed.fastq.gz', 'SLH_AL_0042.R2.trimmed.fastq.gz')
2026-07-22 17:17:26 | INFO | names.py | SLH_AL_0048 <- ('SLH_AL_0048.R1.trimmed.fastq.gz', 'SLH_AL_0048.R2.trimmed.fastq.gz')
2026-07-22 17:17:26 | INFO | names.py | SLH_AL_0063 <- ('SLH_AL_0063.R1.trimmed.fastq.gz', 'SLH_AL_0063.R2.trimmed.fastq.gz')
2026-07-22 17:17:26 | INFO | mapper.py | using existing bwa-mem2 reference index: AmaTu_v01_no00_renamed.fa
2026-07-22 17:17:26 | INFO | mapper.py | mapping 19 samples to coordinate-sorted BAMs in /home/deren/Documents/ipyrad-tests/TUTORIAL/MAP/RAD
2026-07-22 17:17:26 | INFO | mapper.py | using up to 8 cores (up to 2 multi-threaded jobs using 4 threads)
[####################] 100% | Mapping - total jobs: 19
[####################] 100% | Gathering mapping stats - total jobs: 19
2026-07-22 17:33:08 | INFO | mapper.py | mapping stats written to /home/deren/Documents/ipyrad-tests/TUTORIAL/MAP/RAD/ipyrad_map_stats_0.txt and /home/deren/Documents/ipyrad-tests/TUTORIAL/MAP/RAD/ipyrad_map_stats_0.json
The stats file shows the following: Approximately 60% of read pairs were retained in each sample, after removing reads that were either unmapped or not primary alignments, or that did not map to the same scaffold. This file also includes a table below the main stats with a "preview", showing how typical filters that will be applied in the next stage (assemble) will affect these reads. The mapping scores (MAPQ) are quite high (mean 60), and the number of reads that are soft-clipped (reflecting that only part of the read mapped) is generally low. This indicates accurate and unique mapping of reads.
cat TUTORIAL/MAP/RAD/ipyrad_map_stats_0.txt
CMD: ipyrad2 map -d TUTORIAL/TRIM/RAD/SLH_AL_0012.R1.trimmed.fastq.gz TUTORIAL/TRIM/RAD/SLH_AL_0012.R2.trimmed.fastq.gz TUTORIAL/TRIM/RAD/SLH_AL_0013.R1.trimmed.fastq.gz TUTORIAL/TRIM/RAD/SLH_AL_0013.R2.trimmed.fastq.gz ...[truncated; 38 total matched paths] -r TUTORIAL/REFERENCE/AmaTu_v01_no00_renamed.fa -o TUTORIAL/MAP/RAD/ -c 8 -t 4 -f
# ipyrad2 map stats
# Final BAMs are coordinate sorted and indexed.
# Paired-end final BAMs keep only mapped mates on the same scaffold.
## Applied mapping summary
# These counts describe filters already applied during ipyrad2 map.
input_templates reads_removed_unmapped_or_nonprimary reads_removed_same_scaffold_pairing duplicate_records_removed templates_in_final_bam fraction_input_templates_retained_in_final_bam
sample
SLH_AL_0012 290153 107494 83133 0 194840 0.672
SLH_AL_0013 75545 30878 22685 0 48764 0.645
SLH_AL_0014 226714 78384 61470 0 156787 0.692
SLH_AL_0018 206146 75981 56979 0 139666 0.678
SLH_AL_0030 274253 94098 74132 0 190138 0.693
SLH_AL_0034 471707 166676 130923 0 322908 0.685
SLH_AL_0036 286987 99038 80581 0 197178 0.687
SLH_AL_0042 269676 89208 71256 0 189444 0.702
SLH_AL_0048 195509 72579 53924 0 132258 0.676
SLH_AL_0063 175750 83593 61027 0 103440 0.589
SLH_AL_0064 385654 191051 144909 0 217674 0.564
SLH_AL_0084 136286 69609 47522 0 77721 0.570
SLH_AL_0100 342401 163709 126075 0 197509 0.577
SLH_AL_0101 487776 238841 184651 0 276030 0.566
SLH_AL_0104 396203 190541 137683 0 232091 0.586
SLH_AL_0105 288765 130067 99683 0 173890 0.602
SLH_AL_0106 365910 170894 128175 0 216376 0.591
SLH_AL_3065 106854 47885 33100 0 66362 0.621
SLH_AL_3066 251002 112340 85804 0 151930 0.605
## Assemble read-filter preview (not applied during mapping)
# These preview thresholds were not applied during mapping.
# Use them to guide ipyrad2 assemble read filters: -qm/--min-map-q, -ms/--max-softclip, -me/--max-nm, -mt/--max-tlen.
# Preview mode: pair-level thresholds evaluated on final BAM templates.
# MAPQ threshold: 20
# Soft-clipped bases threshold: 25
# NM threshold: 50
# Absolute TLEN threshold: 2000
### Preview filter effects
templates_failing_min_mapq_20 templates_failing_max_softclip_25 templates_failing_max_nm_50 templates_failing_max_abs_tlen_2000 templates_passing_all_preview_filters fraction_templates_passing_all_preview_filters
sample
SLH_AL_0012 18856 35798 24 5254 146946 0.754
SLH_AL_0013 3552 11407 1 1228 35581 0.730
SLH_AL_0014 13796 27875 18 3773 120088 0.766
SLH_AL_0018 12597 26094 15 3459 105733 0.757
SLH_AL_0030 17494 33001 23 4410 145537 0.765
SLH_AL_0034 26239 56760 57 6696 249280 0.772
SLH_AL_0036 21345 34426 31 4615 147784 0.749
SLH_AL_0042 18850 32395 38 4392 144192 0.761
SLH_AL_0048 9749 24783 16 3057 101933 0.771
SLH_AL_0063 9155 31789 13 1953 68071 0.658
SLH_AL_0064 19200 69365 72 4459 141478 0.650
SLH_AL_0084 7132 25495 32 1603 50155 0.645
SLH_AL_0100 18499 60753 71 4125 129355 0.655
SLH_AL_0101 27357 86969 113 6173 178390 0.646
SLH_AL_0104 24521 74828 48 7214 148878 0.641
SLH_AL_0105 16023 51910 46 3462 115442 0.664
SLH_AL_0106 19855 66010 79 4528 142986 0.661
SLH_AL_3065 6075 20527 40 1614 43804 0.660
SLH_AL_3066 13328 45124 29 2870 101385 0.667
### Preview metric summaries
min_mapq_mean min_mapq_median min_mapq_stdev max_softclip_mean max_softclip_median max_softclip_stdev max_nm_mean max_nm_median max_nm_stdev abs_tlen_mean abs_tlen_median abs_tlen_stdev
sample
SLH_AL_0012 50.970 60.000 17.228 14.637 0.000 29.928 4.848 3.000 5.213 815719.101 262.000 6146044.205
SLH_AL_0013 51.509 60.000 15.184 19.401 0.000 34.062 4.088 2.000 4.780 985999.414 224.000 6883261.900
SLH_AL_0014 51.535 60.000 16.697 14.028 0.000 28.978 4.767 3.000 5.145 690880.530 254.000 5657727.339
SLH_AL_0018 51.456 60.000 16.695 14.884 0.000 29.886 4.777 3.000 5.199 824328.422 253.000 6229009.670
SLH_AL_0030 51.486 60.000 16.991 13.604 0.000 28.629 4.827 3.000 5.233 647552.637 259.000 5442898.687
SLH_AL_0034 52.095 60.000 16.261 13.824 0.000 28.882 4.742 3.000 5.157 596535.918 255.000 5248795.868
SLH_AL_0036 50.212 60.000 18.138 13.714 0.000 28.759 4.810 3.000 5.178 647023.665 259.000 5409961.391
SLH_AL_0042 50.963 60.000 17.533 13.275 0.000 27.991 4.900 3.000 5.207 633754.676 257.000 5401961.524
SLH_AL_0048 52.728 60.000 15.483 15.092 0.000 30.403 4.782 3.000 5.201 726915.591 255.000 5844245.247
SLH_AL_0063 51.002 60.000 16.744 22.992 2.000 33.322 8.009 7.000 6.073 164400.919 238.000 1984768.225
SLH_AL_0064 50.521 60.000 16.744 24.195 3.000 34.304 8.006 7.000 6.234 203219.342 248.000 2246946.658
SLH_AL_0084 50.532 60.000 16.940 25.440 4.000 35.474 7.920 7.000 6.347 199785.962 232.000 2189641.413
SLH_AL_0100 50.335 60.000 17.136 22.938 2.000 33.201 8.187 7.000 6.140 200412.323 250.000 2223153.129
SLH_AL_0101 50.098 60.000 17.467 23.637 3.000 33.793 8.439 8.000 6.228 214730.168 257.000 2282749.335
SLH_AL_0104 50.252 60.000 17.688 24.738 4.000 34.836 8.352 8.000 6.171 755339.140 248.000 5696474.467
SLH_AL_0105 50.918 60.000 17.062 22.015 2.000 32.360 8.266 7.000 6.087 185289.978 247.000 2116470.481
SLH_AL_0106 50.898 60.000 16.997 22.937 2.000 33.400 8.534 8.000 6.251 193010.700 257.000 2161833.714
SLH_AL_3065 50.888 60.000 16.822 24.089 3.000 34.795 7.922 7.000 6.360 614217.356 228.000 5205936.882
SLH_AL_3066 51.208 60.000 16.740 22.099 2.000 32.683 8.322 8.000 6.083 182257.623 252.000 2137144.878
map WGS data
Next map the trimmed WGS fastqs to the reference genome. Here -m will remove PCR duplicates based on mapping coordinates,
a feature we can apply for WGS reads but not for RAD reads.
ipyrad2 map \
-d TUTORIAL/TRIM/WGS/*.fastq.gz \
-r TUTORIAL/REFERENCE/AmaTu_v01_no00_renamed.fa \
-o TUTORIAL/MAP/WGS/ \
-m \
-c 8 -t 4
ipyrad2 map wgs log
2026-07-22 18:58:06 | INFO | cli_main.py | --------------------------------------------------------------
2026-07-22 18:58:06 | INFO | cli_main.py | ----- ipyrad2 map: map reads and write coordinate-sorted BAMs -----
2026-07-22 18:58:06 | INFO | cli_main.py | --------------------------------------------------------------
2026-07-22 18:58:06 | INFO | cli_main.py | CMD: ipyrad2 map -d TUTORIAL/TRIM/WGS/21040XD-01-07_S39_L002.R1.trimmed.fastq.gz TUTORIAL/TRIM/WGS/21040XD-01-07_S39_L002.R2.trimmed.fastq.gz TUTORIAL/TRIM/WGS/21040XD-01-08_S40_L002.R1.trimmed.fastq.gz ...[truncated; 8 total matched paths] -r TUTORIAL/REFERENCE/AmaTu_v01_no00_renamed.fa -o TUTORIAL/MAP/WGS/ -m -c 8 -t 4
2026-07-22 18:58:06 | INFO | names.py | paired files by auto-detecting mate tokens in filenames
2026-07-22 18:58:06 | INFO | names.py | showing first 4/4 names parsed from file paths
2026-07-22 18:58:06 | INFO | names.py | 21040XD-01-07_S39_L002 <- ('21040XD-01-07_S39_L002.R1.trimmed.fastq.gz', '21040XD-01-07_S39_L002.R2.trimmed.fastq.gz')
2026-07-22 18:58:06 | INFO | names.py | 21040XD-01-08_S40_L002 <- ('21040XD-01-08_S40_L002.R1.trimmed.fastq.gz', '21040XD-01-08_S40_L002.R2.trimmed.fastq.gz')
2026-07-22 18:58:06 | INFO | names.py | 21040XD-01-09_S41_L002 <- ('21040XD-01-09_S41_L002.R1.trimmed.fastq.gz', '21040XD-01-09_S41_L002.R2.trimmed.fastq.gz')
2026-07-22 18:58:06 | INFO | names.py | SRR15412865 <- ('SRR15412865.R1.trimmed.fastq.gz', 'SRR15412865.R2.trimmed.fastq.gz')
2026-07-22 18:58:06 | WARNING | mapper.py | removing PCR duplicates by coordinates. Be sure this run includes only WGS samples, not RAD
2026-07-22 18:58:06 | INFO | mapper.py | using existing bwa-mem2 reference index: AmaTu_v01_no00_renamed.fa
2026-07-22 18:58:06 | INFO | mapper.py | mapping 4 samples to coordinate-sorted BAMs in /home/deren/Documents/ipyrad-tests/TUTORIAL/MAP/WGS
2026-07-22 18:58:06 | INFO | mapper.py | using up to 8 cores (up to 2 multi-threaded jobs using 4 threads)
[####################] 100% | Mapping - total jobs: 4
[####################] 100% | Gathering mapping stats - total jobs: 4
2026-07-23 09:26:10 | INFO | mapper.py | mapping stats written to /home/deren/Documents/ipyrad-tests/TUTORIAL/MAP/WGS/ipyrad_map_stats_0.txt and /home/deren/Documents/ipyrad-tests/TUTORIAL/MAP/WGS/ipyrad_map_stats_0.json
The stats report shows that the mapping rate for these samples was approximately ... Many read pairs were excluded becaues they did not map, were not primary alignments, or paired to different scaffolds. Note, this could reflect these samples being more distantly related to the reference genome, rather than being an artifact of being WGS versus RAD.
cat TUTORIAL/MAP/WGS/ipyrad_map_stats_0.txt
CMD: ipyrad2 map -d TUTORIAL/TRIM/WGS/21040XD-01-07_S39_L002.R1.trimmed.fastq.gz TUTORIAL/TRIM/WGS/21040XD-01-07_S39_L002.R2.trimmed.fastq.gz TUTORIAL/TRIM/WGS/21040XD-01-08_S40_L002.R1.trimmed.fastq.gz ...[truncated; 8 total matched paths] -r TUTORIAL/REFERENCE/AmaTu_v01_no00_renamed.fa -o TUTORIAL/MAP/WGS/ -m -c 8 -t 4
# ipyrad2 map stats
# Final BAMs are coordinate sorted and indexed.
# Paired-end final BAMs keep only mapped mates on the same scaffold.
## Applied mapping summary
# These counts describe filters already applied during ipyrad2 map.
input_templates reads_removed_unmapped_or_nonprimary reads_removed_same_scaffold_pairing duplicate_records_removed templates_in_final_bam fraction_input_templates_retained_in_final_bam
sample
21040XD-01-07_S39_L002 6221847 3966472 2741413 347115 2694348 0.433
21040XD-01-08_S40_L002 6120214 3373345 2131772 496787 3119263 0.510
21040XD-01-09_S41_L002 6188210 3921824 2829802 762609 2431094 0.393
SRR15412865 7548622 8714761 4892654 3938 742946 0.098
## Assemble read-filter preview (not applied during mapping)
# These preview thresholds were not applied during mapping.
# Use them to guide ipyrad2 assemble read filters: -qm/--min-map-q, -ms/--max-softclip, -me/--max-nm, -mt/--max-tlen.
# Preview mode: pair-level thresholds evaluated on final BAM templates.
# MAPQ threshold: 20
# Soft-clipped bases threshold: 25
# NM threshold: 50
# Absolute TLEN threshold: 2000
### Preview filter effects
templates_failing_min_mapq_20 templates_failing_max_softclip_25 templates_failing_max_nm_50 templates_failing_max_abs_tlen_2000 templates_passing_all_preview_filters fraction_templates_passing_all_preview_filters
sample
21040XD-01-07_S39_L002 931985 1089614 1605 150000 1146875 0.426
21040XD-01-08_S40_L002 1124354 1111925 1492 135900 1392662 0.446
21040XD-01-09_S41_L002 846003 1105404 1482 158592 1005254 0.413
SRR15412865 414198 618744 1217 141652 91999 0.124
### Preview metric summaries
min_mapq_mean min_mapq_median min_mapq_stdev max_softclip_mean max_softclip_median max_softclip_stdev max_nm_mean max_nm_median max_nm_stdev abs_tlen_mean abs_tlen_median abs_tlen_stdev
sample
21040XD-01-07_S39_L002 34.851 40.000 25.218 33.562 11.000 41.737 9.957 9.000 6.962 454316.974 241.000 3231238.069
21040XD-01-08_S40_L002 33.990 40.000 25.243 29.223 7.000 39.495 9.147 8.000 6.711 297615.529 199.000 2573490.135
21040XD-01-09_S41_L002 34.873 40.000 24.900 37.417 19.000 42.354 10.700 10.000 6.916 415525.864 237.000 2880333.931
SRR15412865 23.402 12.000 24.111 161.495 209.000 85.971 7.367 2.000 10.350 2505987.176 346.000 7198230.542
assemble
We are now ready to assemble the dataset. Here we specify separate paths to the RAD and WGS BAM alignments
using --rad-bams and --wgs-bams, respectively, and specify the path to the reference genome fasta (-r).
We saw in the mapping stats above that the mean MAPQ score was generally >50. Based on this we can confidently
exclude reads with much lower mapping scores, so I raised the -qm parameter to 40.
Most other options are left at their defaults.
Let's also rename our samples at this point so that the final assembled data contains easily interpretable
names, rather than obscure accession IDs, for downstream analyses. To do this we provide an 2-column file
using the --rename flag to map current names to new names.
ipyrad2 assemble \
--rad-bams TUTORIAL/MAP/RAD/*.bam \
--wgs-bams TUTORIAL/MAP/WGS/*.bam \
--reference TUTORIAL/REFERENCE/AmaTu_v01_no00_renamed.fa \
--out TUTORIAL/OUT/ \
--rename TUTORIAL/NAMES.txt \
--name assembly \
-qm 40 \
-c 8 -t 4
ipyrad2 assemble log
2026-07-23 09:32:26 | INFO | cli_main.py | -----------------------------------------------------------
2026-07-23 09:32:26 | INFO | cli_main.py | ----- ipyrad2 assemble: delimit loci and call variants -----
2026-07-23 09:32:26 | INFO | cli_main.py | -----------------------------------------------------------
2026-07-23 09:32:26 | INFO | cli_main.py | CMD: ipyrad2 assemble --rad-bams TUTORIAL/MAP/RAD/SLH_AL_0012.trimmed.sorted.bam TUTORIAL/MAP/RAD/SLH_AL_0013.trimmed.sorted.bam TUTORIAL/MAP/RAD/SLH_AL_0014.trimmed.sorted.bam TUTORIAL/MAP/RAD/SLH_AL_0018.trimmed.sorted.bam TUTORIAL/MAP/RAD/SLH_AL_0030.trimmed.sorted.bam ...[truncated; 19 total matched paths] --wgs-bams TUTORIAL/MAP/WGS/21040XD-01-07_S39_L002.trimmed.sorted.bam TUTORIAL/MAP/WGS/21040XD-01-08_S40_L002.trimmed.sorted.bam TUTORIAL/MAP/WGS/21040XD-01-09_S41_L002.trimmed.sorted.bam TUTORIAL/MAP/WGS/SRR15412865.trimmed.sorted.bam --reference TUTORIAL/REFERENCE/AmaTu_v01_no00_renamed.fa --out TUTORIAL/OUT/ --name assembly -qm 40 -c 8 -t 4
2026-07-23 09:32:26 | ERROR | cli_main.py | Error: outfiles with prefix assembly already exist in /home/deren/Documents/ipyrad-tests/TUTORIAL/OUT. Use --force to overwrite.
2026-07-23 09:32:26 | ERROR | cli_main.py | see error message above. Shutting down.
(ipyrad2) deren@rex ~/Documents/ipyrad-tests $ ipyrad2 assemble --rad-bams TUTORIAL/MAP/RAD/*.bam --wgs-bams TUTORIAL/MAP/WGS/*.bam --reference TUTORIAL/REFERENCE/AmaTu_v01_no00_renamed.fa --out TUTORIAL/OUT/ --name assembly -qm 40 -c 8 -t 4 -f
2026-07-23 09:32:29 | INFO | cli_main.py | -----------------------------------------------------------
2026-07-23 09:32:29 | INFO | cli_main.py | ----- ipyrad2 assemble: delimit loci and call variants -----
2026-07-23 09:32:29 | INFO | cli_main.py | -----------------------------------------------------------
2026-07-23 09:32:29 | INFO | cli_main.py | CMD: ipyrad2 assemble --rad-bams TUTORIAL/MAP/RAD/SLH_AL_0012.trimmed.sorted.bam TUTORIAL/MAP/RAD/SLH_AL_0013.trimmed.sorted.bam TUTORIAL/MAP/RAD/SLH_AL_0014.trimmed.sorted.bam TUTORIAL/MAP/RAD/SLH_AL_0018.trimmed.sorted.bam TUTORIAL/MAP/RAD/SLH_AL_0030.trimmed.sorted.bam ...[truncated; 19 total matched paths] --wgs-bams TUTORIAL/MAP/WGS/21040XD-01-07_S39_L002.trimmed.sorted.bam TUTORIAL/MAP/WGS/21040XD-01-08_S40_L002.trimmed.sorted.bam TUTORIAL/MAP/WGS/21040XD-01-09_S41_L002.trimmed.sorted.bam TUTORIAL/MAP/WGS/SRR15412865.trimmed.sorted.bam --reference TUTORIAL/REFERENCE/AmaTu_v01_no00_renamed.fa --out TUTORIAL/OUT/ --name assembly -qm 40 -c 8 -t 4 -f
2026-07-23 09:32:29 | INFO | assemble.py | loading BAM inputs
2026-07-23 09:32:29 | INFO | assemble.py | loaded 19 RAD samples
2026-07-23 09:32:29 | INFO | assemble.py | loaded 4 WGS samples
[####################] 100% | Scanning BAM headers - total jobs: 23
2026-07-23 09:32:31 | INFO | assemble.py | BAM layout: 23 paired-end, 0 single-end
2026-07-23 09:32:34 | INFO | assemble.py | validating BAM headers against the reference
2026-07-23 09:32:34 | INFO | assemble.py | filtering mapped reads before assembly: MAPQ>=40, same scaffold pairs only, abs(TLEN)<=1000
[####################] 100% | Filtering mapped reads - total jobs: 23
2026-07-23 09:33:41 | INFO | assemble.py | filtered analysis BAMs ready for 23 samples
2026-07-23 09:33:41 | INFO | assemble.py | using up to 8 cores (2 concurrent jobs, 4 threads per job)
2026-07-23 09:33:41 | INFO | assemble.py | building per-sample coverage BEDs
[####################] 100% | Building per-sample coverage BEDs - total jobs: 23
2026-07-23 09:36:11 | INFO | assemble.py | building loci from shared sample coverage BEDs
2026-07-23 09:36:13 | INFO | assemble.py | scoring paralog evidence
2026-07-23 09:36:19 | INFO | assemble.py | mixed RAD/WGS assembly detected; skipping softclip-based paralog failure for WGS samples
2026-07-23 09:36:19 | INFO | assemble.py | paralog scoring uses the shared loci BED for all samples
2026-07-23 09:36:19 | INFO | assemble.py | preparing loci-restricted BAMs for paralog scoring
[####################] 100% | Preparing loci-restricted paralog BAMs - total jobs: 23
2026-07-23 09:36:34 | INFO | assemble.py | loci-restricted paralog BAMs ready for 23 samples
[####################] 100% | Scoring paralog evidence - total jobs: 23
2026-07-23 09:40:34 | INFO | assemble.py | aggregating paralog filters across samples
2026-07-23 09:40:34 | INFO | assemble.py | mixed RAD/WGS assembly detected; using RAD samples to control shared paralog locus retention and WGS samples for QC only
2026-07-23 09:40:37 | INFO | assemble.py | paralog filtering retained 10693/12008 shared loci
2026-07-23 09:40:37 | INFO | assemble.py | preparing cleaned BAMs for joint calling
[####################] 100% | Preparing cleaned calling BAMs - total jobs: 23
2026-07-23 09:40:50 | INFO | assemble.py | cleaned calling BAMs ready for 23 samples
[####################] 100% | Calling variants - total jobs: 8
2026-07-23 09:42:52 | INFO | assemble.py | filtering variant calls
2026-07-23 09:42:56 | INFO | assemble.py | masking WGS heterozygous genotypes by allele balance
2026-07-23 09:43:00 | INFO | assemble.py | masked 708 / 3008 WGS heterozygous genotypes outside allele-balance range [0.20, 0.80]
2026-07-23 09:43:00 | INFO | assemble.py | resolving indels and SNPs
2026-07-23 09:43:15 | INFO | variants.py | masked 598 overlapping-indel clusters (1317 records, 6249 bp)
[####################] 100% | Building low-depth masks - total jobs: 23
[####################] 100% | Building sample-specific paralog masks - total jobs: 23
[####################] 100% | Merging sample masks - total jobs: 23
2026-07-23 09:43:20 | INFO | assemble.py | preparing locus reference sequence
2026-07-23 09:43:20 | INFO | assemble.py | building consensus sequences
[####################] 100% | Building consensus sequences - total jobs: 23
2026-07-23 09:43:30 | INFO | assemble.py | building locus database
2026-07-23 09:43:30 | INFO | assemble.py | built locus database from 24 FASTA inputs
2026-07-23 09:43:30 | INFO | assemble.py | writing final loci and summary files
[####################] 100% | Resolving and writing final loci - total jobs: 84
2026-07-23 09:44:02 | INFO | assemble.py | wrote final loci: 8699 loci, 2797293 sites
2026-07-23 09:44:02 | INFO | assemble.py | writing final VCF
[####################] 100% | Building final VCF masks - total jobs: 23
2026-07-23 09:44:05 | INFO | variants.py | masking final VCF chunks
[####################] 100% | Masking final VCF chunks - total jobs: 32
2026-07-23 09:44:13 | INFO | variants.py | concatenating masked final VCF chunks
2026-07-23 09:44:14 | INFO | assemble.py | wrote final VCF
2026-07-23 09:44:17 | INFO | assemble.py | writing SNP database
[####################] 100% | Building SNP database chunks - total jobs: 16
2026-07-23 09:44:30 | INFO | assemble.py | wrote SNP database with 292466 SNP sites
2026-07-23 09:44:30 | INFO | assemble.py | preparing final sample depth summaries
[####################] 100% | Preparing final depth summaries - total jobs: 23
2026-07-23 09:44:31 | INFO | assemble.py | summarizing final sample depth
[####################] 100% | Summarizing final sample depth - total jobs: 23
2026-07-23 09:44:33 | INFO | assemble.py | final sample depth summary ready for 23 samples
2026-07-23 09:44:33 | INFO | loci.py | wrote assemble summary report
2026-07-23 09:44:33 | INFO | assemble.py | removed assemble tmpdir /home/deren/Documents/ipyrad-tests/TUTORIAL/OUT/assembly_tmpdir
2026-07-23 09:44:33 | INFO | assemble.py | assemble complete; outputs written to /home/deren/Documents/ipyrad-tests/TUTORIAL/OUT
The stats file report shows:
Assembly stats
We now have a finished assembly stored in TUTORIAL/OUT/. The first thing to do is to look at the
human-readable stats file.
cat TUTORIAL/OUT/assembly.stats.txt
CMD: ipyrad2 assemble --rad-bams TUTORIAL/MAP/RAD/SLH_AL_0012.trimmed.sorted.bam TUTORIAL/MAP/RAD/SLH_AL_0013.trimmed.sorted.bam TUTORIAL/MAP/RAD/SLH_AL_0014.trimmed.sorted.bam TUTORIAL/MAP/RAD/SLH_AL_0018.trimmed.sorted.bam TUTORIAL/MAP/RAD/SLH_AL_0030.trimmed.sorted.bam ...[truncated; 19 total matched paths] --wgs-bams TUTORIAL/MAP/WGS/21040XD-01-07_S39_L002.trimmed.sorted.bam TUTORIAL/MAP/WGS/21040XD-01-08_S40_L002.trimmed.sorted.bam TUTORIAL/MAP/WGS/21040XD-01-09_S41_L002.trimmed.sorted.bam TUTORIAL/MAP/WGS/SRR15412865.trimmed.sorted.bam --reference TUTORIAL/REFERENCE/AmaTu_v01_no00_renamed.fa --out TUTORIAL/OUT/ --name assembly -qm 40 -c 8 -t 4 -f
# Assemble Summary
Samples 23
Shared loci before minimum sample coverage filter 26,905
Shared loci after delimiting 12,008
Shared loci after paralog filtering 10,693
Final loci written 8,699
Final loci retained fraction after paralog filtering 0.813523
Final loci retained fraction after delimiting 0.724434
Assembled sites 2,797,293
Final SNP sites written 292,466
Variable sites 156,941
Phylogenetically informative sites 64,231
Alignment matrix occupancy fraction 0.360839
Overlapping indel clusters masked 598
Overlapping indel records removed 1,317
Overlapping indel bases masked 6,249
# Mixed RAD/WGS Diagnostics
RAD samples 19
WGS samples 4
Loci failed by RAD paralog QC 1,315
Loci failed by WGS paralog QC 704
Loci failed by RAD and WGS paralog QC 157
Loci kept by RAD but failed by WGS QC 547
WGS heterozygous genotypes masked by allele balance 708
Sites supported by RAD only 140,754
Sites supported by WGS only 7,477
Sites supported by RAD and WGS 8,608
Sites supported by neither RAD nor WGS 135,627
# Locus Filtering
Loci filtered by minimum length 7
Loci filtered by minimum sample coverage 14,897
Loci filtered by maximum variant frequency 0
Loci filtered by maximum shared heterozygosity 1,992
Loci filtered by maximum depth outlier 0
# Sample Masking
Loci with samples masked by minimum observed fraction threshold 1,384
Sample masks triggered by minimum observed fraction threshold 1,547
Loci with samples masked by sample heterozygosity threshold 5
Sample masks triggered by sample heterozygosity threshold 5
# Alignment Summary
Mean locus length 321.565
Median locus length 289.000
Minimum locus length 27
Maximum locus length 1,631
Mean samples per locus 9.522
Median samples per locus 8.000
Sites with sample coverage >= 2 2,715,376
Sites with sample coverage >= 3 2,706,445
Sites with sample coverage >= 4 2,695,768
Sites with sample coverage >= trim minimum 2,695,768
# Sample Summary
Sample Sample type Read layout Reads before filtering Reads after filtering Loci in alignment Loci fraction in alignment Shared loci with nonzero depth Shared-depth loci fraction Mean depth in shared loci Median depth in shared loci Mean depth in nonzero shared loci Median depth in nonzero shared loci Masked by minimum observed fraction threshold Masked by sample heterozygosity threshold
21040XD-01-07_S39_L002 WGS PE 5,388,695 3,073,781 2,340 0.268996 2,852 0.327854 0.874 0.000 2.666 1.737 509 2
21040XD-01-08_S40_L002 WGS PE 6,238,525 3,453,715 1,708 0.196344 2,242 0.257731 0.606 0.000 2.352 1.336 533 1
21040XD-01-09_S41_L002 WGS PE 4,862,185 2,765,049 1,435 0.164961 1,836 0.211059 0.551 0.000 2.609 1.450 401 0
SLH_AL_0012 RAD PE 389,680 339,937 4,094 0.470629 4,096 0.470859 7.787 0.000 16.538 9.000 5 0
SLH_AL_0013 RAD PE 97,528 88,684 388 0.044603 389 0.044718 0.801 0.000 17.915 5.000 1 0
SLH_AL_0014 RAD PE 313,574 276,308 3,752 0.431314 3,758 0.432004 6.209 0.000 14.373 8.000 9 0
SLH_AL_0018 RAD PE 279,332 246,319 3,358 0.386021 3,358 0.386021 5.465 0.000 14.157 7.291 0 0
SLH_AL_0030 RAD PE 380,276 333,838 4,126 0.474307 4,134 0.475227 7.547 0.000 15.882 9.374 6 1
SLH_AL_0034 RAD PE 645,816 575,161 4,824 0.554546 4,826 0.554776 13.640 6.000 24.587 14.396 3 1
SLH_AL_0036 RAD PE 394,356 337,531 4,106 0.472008 4,107 0.472123 7.279 0.000 15.418 9.000 2 0
SLH_AL_0042 RAD PE 378,888 328,846 4,109 0.472353 4,111 0.472583 7.184 0.000 15.202 9.000 4 0
SLH_AL_0048 RAD PE 264,516 238,431 3,306 0.380044 3,311 0.380618 5.517 0.000 14.494 8.000 6 0
SLH_AL_0063 RAD PE 206,880 182,070 3,750 0.431084 3,751 0.431199 5.248 0.000 12.170 8.000 2 0
SLH_AL_0064 RAD PE 435,348 382,907 5,934 0.682147 5,935 0.682262 13.198 9.000 19.345 13.313 1 0
SLH_AL_0084 RAD PE 155,442 136,433 1,950 0.224164 1,957 0.224968 2.942 0.000 13.077 6.928 7 0
SLH_AL_0100 RAD PE 395,018 343,862 5,894 0.677549 5,895 0.677664 11.896 9.000 17.554 13.000 1 0
SLH_AL_0101 RAD PE 552,060 477,004 6,174 0.709737 6,174 0.709737 16.592 13.000 23.378 18.000 2 0
SLH_AL_0104 RAD PE 464,182 400,608 3,973 0.456719 3,976 0.457064 9.799 0.000 21.439 13.000 5 0
SLH_AL_0105 RAD PE 347,780 304,528 4,986 0.573169 4,988 0.573399 9.468 6.000 16.513 12.000 3 0
SLH_AL_0106 RAD PE 432,752 378,310 6,009 0.690769 6,009 0.690769 13.149 10.410 19.036 15.000 1 0
SLH_AL_3065 RAD PE 132,724 116,456 1,805 0.207495 1,811 0.208185 2.473 0.000 11.878 6.000 7 0
SLH_AL_3066 RAD PE 303,860 267,303 4,669 0.536728 4,671 0.536958 8.188 5.000 15.249 11.000 2 0
SRR15412865 WGS PE 1,485,892 580,822 141 0.016209 178 0.020462 0.078 0.000 3.798 1.535 37 0
# Locus Occupancy
Samples with data RAD loci before min sample coverage RAD loci after min sample coverage Final filtered RAD loci with WGS Cumulative final loci Fraction of final loci
0 0 0 0 0 0.000000
1 9,138 0 0 0 0.000000
2 3,313 0 0 0 0.000000
3 2,238 0 0 0 0.000000
4 1,829 1,798 940 940 0.108058
5 1,380 1,370 981 1,921 0.112772
6 1,220 1,203 784 2,705 0.090125
7 1,407 1,406 1,009 3,714 0.115990
8 1,346 1,349 883 4,597 0.101506
9 778 749 627 5,224 0.072077
10 587 545 548 5,772 0.062996
11 417 389 394 6,166 0.045293
12 356 340 299 6,465 0.034372
13 376 366 259 6,724 0.029774
14 448 448 286 7,010 0.032877
15 461 470 343 7,353 0.039430
16 473 460 330 7,683 0.037935
17 500 493 356 8,039 0.040924
18 488 475 337 8,376 0.038740
19 150 147 183 8,559 0.021037
20 0 0 82 8,641 0.009426
21 0 0 24 8,665 0.002759
22 0 0 27 8,692 0.003104
23 0 0 7 8,699 0.000805
We should be pretty satisifed with this result. We recovered many loci and without too much missing data -- i.e., most loci have data from nearly all samples, not just a subset of them. These loci seem to be highly variable, with nearly X variant sites recovered.
Assembled loci
After examining the stats file the next step should be to look at the loci file, which provides
a human-readable format for examining aligned loci to ensure that they look reasonable. This is
a large file so bash command-line tools like less or head are often useful for viewing it.
[describe loci format]
zcat TUTORIAL/OUT/assembly.loci.gz | head -n 202
assembly_reference_sequence TGTGAGTAATATTTGATGTTGAATAGTAAATGAAATATATTCCTATTTAAGGGGGGGTGTCCAAGACACCATTAAAACTTATGTTCAAATCCTTTCATTTCATAAAGCTAAGAATGAATACCTCAGTTACTAACATAACAATATAACATGCATATAGCCCACATCTATGCCCAGAATCAGACCATAATATACACAATTTTAATCAAGTAAACTCTAAAAATTCATTCATAAGAATACTATCAAGCAAGCAATAGCAACGCAAAACACAAAATCAATTCAAAACCCTTAAAAATAAAATAAGAAACAAC
SLH_AL_0013 TGTGAGTAATATTTGATGTTGAATAGTAAATGAAATATATTCCTATTTANGGGGNGNTGTCCAAGACNCCATTAAAACNTATGTTCAAATCCTTTCATTTCATAAAGCTAANAATGAANACCNCAGTTACTAACATAACAATATAACATGCATATAGCCCACATCTATGCCCAGAATCAGACCATAATATACACAATTTTAATCAAGTAAAMTCTAAAAATTCATTCATAAGAATACTATCAAGCAAGCAATAGCAACGSAAAACACAAAATCAATTCAAAACNNNNNNNNNNNNNNNNNNNNNNNNN
SLH_AL_0042 TGTGAGTAATATTTGATGTTGAATAGTAAATGAAATATATTCCTATTTAGGGGGGGGTGTCCAAGACACCATTAAAACTTATGTTCAAATCCTTTCATTTCATAAAGCTAAGAATGAATACCTCAGTTACTAACATAACAATATAACATGCATATAGCCCACATCTATGCCCAGAATCAGACCATAATATACACAATTTTAATCAAGTAAACTCTAAAAATTCATTCATAAGAATACTATCAAGCAAGCAATAGCAACGCAAAACACAAAATCAATTCAAAACCCTTTAAAATAAAATAAGAAACAAC
SLH_AL_0063 TGTGAATAATATTTCATGTTGAATAGTAAATGAAATACATTCCTATTTAAGGGGAGCTGTCCAAGACTCCATTAAAACATATGTTCAAATCCTTTCATTTCATAAAGCTAAGAATGAACACCTCAGTTACTAACATAACAATATAACATGCATATAGCCCACATCTATGCCCAGAATCAGACTATAATATCCACAATTTTAATCAAGTAAACACTAAAAATTCATTCATAAGAATACTATCAAGCAAGCAATAGCAACGCAAAACACAAAATCAATTCAAAACCCTTTAAAATAAAATAAGAAACAAC
SLH_AL_0084 TGTGAGTAATATTTGATGTTAAATAGTAAATGAAATAAATTCCTATTTAAGGGGGGGTGTCCAAGACACCATTAAAACTTATGTTCAAATCCTTTCATTTCATAAAGCTAAGAATGAACACCTCAGTTACTAACATAACAATATAACATGCATATAGCCCACATCTATGCCCAGAATCAGACCATAATATACACAATTTTAATCAAGTAAACTCTAAAAATTCATTCATAAGAATACTATCAAGCAAGCAATAGCAACGCAAAACACAAAATCAATTCAAAACTTTTTAAAATAAAATAAGAAACAAN
SLH_AL_0104 TGTGAGTAA-ATTTGATGTTGAATAGTAAATGAAATATATTCCTATTTAAGGGGGGGTGTCCAAGACACCATTAAAACTTATGTTCAAATCCTTTCATTTCATAAAGCTAAGAATGAATACCTCAGTTACTAACATAACAATATAACATGCATATAGCCCACATCTATGCCCAGAATCAGACCATAATATACACAATTTTAATCAAGTAAACTCTAAAAATTCATTCATAAGAATACTATCAAGCAAGCAATAGCAACGCAAAACACAAAACCAATTCAAAACCCTTTAAAATAAAATAAGAAACAAC
SLH_AL_0105 TGTGAATAATATTTCATGTTGAATAGTAAATGAAATACATTCCTATTTAAGGGGAGCTGTCCAAGACTCCATTAAAACATATGTTCAAATCCTTTCATTTCATAAAGCTAAGAATGAACACCTCAGTTACTAACATAACAATATAACATGCATATAGCCCACATCTATGCCCAGAATCAGACTATAATATCCACAATTTTAATCAAGTAAACACTAAAAATTCATTCATAAGAATACTATCAAGCAAGCAATAGCAACGCAAAACACAAAATCAATTCAAAACCCTTTAAAATAAAATAAGAAACAAC
// * * - * - * * * * * * * -* - - -- - |0:A_tuberculatus_Chr01:17883-18190
assembly_reference_sequence GCCTTGCCTATAATTCTCCTAAACTTTTACACTCTTTGTGGGTACTATCATGTTATTTGGGTTGATAAAACCTCTTGCTCTAGTCAAATTGCTCACATGTGCAATGATGTGTGTCAAATATGACAGACAAAACAAGGCTCTTTTAGCTCATTATGTGGCCTTCTTGCTGCCATATATAGTTTTCTAGGTCATAGTGACCCAAATGAAGATTTCTATGTTGCATTCTCACATTGCCATAAAAAATTTTGAAACACTGCAA
SLH_AL_0063 GCCTTGCCTATAGTTCTCCTAAACTTTTACACTCTTTGTGGGTACTATCATGTTATTTGGCTTGATAAAACCTCTTGGTCTAGTCAAACTGCTCACATATGCAATGATGCGTGTCTAATATGACAGACAAAACAAGGCTCTTTTAGCTCATTATGTGGCTTTCTTGCTGCCATGTATAGTTTTCTAGGTCNAAGTGACCCAAATGAAGATTTCTATGTTGCATTCTCACATTGCCATAAAAGATTTAGAAACACTGCAA
SLH_AL_0064 GCCTTGCCTATAGTTCTCCTAAACTTTTACACTCTTTGTGGGTACTATCATGTTATTTGGCTTGATAAAACCTCTTGGTCTAGTCAAACTGCTCACATATGCAATGATGTGTGTCTAATATGACAGACAAAACAAGGCTCTTTTAGCTCATTATGTGGCTTTCTTGCTGCCATGTATAGTTTTCTAGGTCNAAGTGACCCAAATGAAGATTTCTATGTTGCATTCTCACATTGCCATAAAAGATTTAGAAACACTGCAA
SLH_AL_0100 GCCTTGCCTATAGTTCTCCTAAACTTTTACACTCTTTGTGGGTACTATCATGTTATTTGGCTTGATAAAACCTCTTGGTCTAGTCAAACTGCTCACATATGCAATGATGTGTGTCTAATATGACAGACAAAACAAGGCTCTTTTAGCTCATTATGTGGCTTTCTTGCTGCCATGTATAGTTTTCTAGGTCNAAGTGACCCAAATGAAGATTTCTATGTTGCATTCTCACATTGCCATAAAAGATTTAGAAACACTGCAA
SLH_AL_0101 GCCTTGCCTATAGTTCTCCTAAACTTTTACACTCTTTGTGGGTACTATCATGTTATTTGGCTTGATAAAACCTCTTGGTCTAGTCAAACTGCTCACATATGCAATGATGTGTGTCTAATATGACAGACAAAACAAGGCTCTTTTAGCTCATTATGTGGCTTTCTTGCTGCCATGTATAGTTTTCTAGGTCNAAGTGACCCAAATGAAGATTTCTATGTTGCATTCTCACATTGCCATAAAAGATTTAGAAACACTGCAA
SLH_AL_0104 GCCTTTCCTATAGTTCTCCTAAACTTTTACACTCTTTGTGGGTTCTATCATGTTATTTGGCTTGATAAAACCTCTTGGTCTAGTCAAACTGCTCACATATGCAATGATGTGTGTCNAATATGACAGACAAAACAAGGCTCTT-------ATTATGTGGCCTTCTTGCTGCCATGTATAGTTTTCTAGGTCNTAGTGACCCAAATGAAGATTTCTATGTTGCATTCTCACATTGCCATAAAAAATTTAGATACACTGCAA
SLH_AL_0105 GCCTTGCCTATAGTTCTCCTAAACTTTTACACTCTTTGTGGGTACTATCATGTTATTTGGCTTGATAAAACCTCTTGGTCTAGTCAAACTGCTCACATATGCAATGATGCGTGTCTAATATGACAGACAAAACAAGGCTCTTTTAGCTCATTATGTGGCTTTCTTGCTGCCATGTATAGTTTTCTAGGTCNAAGTGACCCAAATGAAGATTTCTATGTTGCATTCTCACATTGCCATAAAAGATTTAGAAACACTGCAA
SLH_AL_0106 GCCTTGCCTATAGTTCTCCTAAACTTTTACACTCTTTGTGGGTACTATCATGTTATTTGGCTTGATAAAACCTCTTGGTCTAGTCAAACTGCTCACATATGCAATGATGTGTGTCTAATATGACAGACAAAACAAGGCTCTTTTAGCTCATTATGTGGCTTTCTTGCTGCCATGTATAGTTTTCTAGGTCNAAGTGACCCAAATGAAGATTTCTATGTTGCATTCTCACATTGCCATAAAAGATTTAGAAACACTGCAA
SLH_AL_3066 GCCTTGCCTATAGTTCTCCTAAACTTTTACACTCTTTGTGGGTACTATCATGTTATTTGGCTTGATAAAACCTCTTGGTCTAGTCAAACTGCTCACATATGCAATGATGCGTGTCTAATATGACAGACAAAACAAGGCTCTTTTAGCTCATTATGTGGCTTTCTTGCTGCCATGTATAGTTTTCTAGGTCNAAGTGACCCAAATGAAGATTTCTATGTTGCATTCTCACATTGCCATAAAAGATTTAGAAACACTGCAA
// - - - - - - - * - * - * * - - |1:A_tuberculatus_Chr01:98725-98983
assembly_reference_sequence ATTCATGTTTCTTGTTTTTCTCTGATAAACCCTGTTTCTTCTAGTAAACCCACAAGCAAAGCTCCATTTCCTTAACCTCCTCCCAAACAAACACTCCCAACTTATTGTTTCTTCATCATATGTGCCAATCAATTCTTTGTCCAAAAACCTATTTAAAAACCATTACCATATTCATTACGTATGCCCATTGATATTCGATTC
SLH_AL_0063 NTTCATGTTTCTCGTTTTCCTCTGATAANCCCTGTTTCTTCGAGTAAACCCACAAGCAAAGCTCCATTTCCTTANCCTCCTCCCAAACAAACACTCCCANCTTATTGTTTGTTCATCATATGTGCCAATCAATTCTTTGTCCAAGAACCCATATAAAAACCATTACCATATTCATTACATATGCCCATTGATATTCAATTC
SLH_AL_0064 ATTCATGTTTCTCGTTTTCCTCTGATAANCCCTGTTTCTTCGAGTAAACCCACAAGCAAAGCTCCATTTCCTTANCCTCCTCCCAAACAAACACTCCCANCTTATTGTTTGTTCATCATATGTGCCAATCAATTCTTTGTCCAAGAACCCATATAAAAACCATTACCATATTCATTACATATGCCCATTGATATTCAATTC
SLH_AL_0084 ATTCATGTTTCTCGTTTTMCTCTGATAANCCCTGTTTCTTCRAGTAAACCCACAAGCAAAGCTCCATTTCCTTANCCTCCTCCCAAACAAACACTCCCANCTTATTGTTTGTTCATCAWATGTGCCAATCAATTCTTTGTCCNAGAACCCATATAAAAACCATTACCATATTCATTACRTATGCCCATTGATATTCAATTC
SLH_AL_0100 ATTCATGTTTCTCGTTTTCCTCTGATAANCCCTGTTTCTTCGAGTAAACCCACAAGCAAAGCTCCATTTCCTTANCCTCCTCCCAAACAAACACTCCCANCTTATTGTTTGTTCATCATATGTGCCAATCAATTCTTTGTCCAAGAACCCATATAAAAACCATTACCATATTCATTACATATGCCCATTGATATTCAATTC
SLH_AL_0101 ATTCATGTTTCTCGTTTTCCTCTGATAANCCCTGTTTCTTCGAGTAAACCCACAAGCAAAGCTCCATTTCCTTANCCTCCTCCCAAACAAACACTCCCANCTTATTGTTTGTTCATCATATGTGCCAATCAATTCTTTGTCCAAGAACCCATATAAAAACCATTACCATATTCATTACATATGCCCATTGATATTCAATTC
SLH_AL_0104 NNNNNNNNNNNNNGTTTTCCTCTGATAANCCCTGTTTCTTCAAGTAAACCCACAAGCAAAGCTCCATTTCCTTANCCTCCTCCCAAACAAAMACTCCCANCTTATTGTTTGTTCATCATATGTGCCAATCAATTCTTTGTCCNANAACCNATNTAAAAACCATTACCATATTCATTACGTATGCCCATTGATATTCAATTC
SLH_AL_0105 NTTCATGTTTCTCGTTTTCCTCTGATAANCCCTGTTTCTTCGAGTAAACCCACAAGCAAAGCTCCATTTCCTTANCCTCCTCCCAAACAAACACTCCCANCTTATTGTTTGTTCATCATATGTGCCAATCAATTCTTTGTCCAAGAACCCATATAAAAACCATTACCATATTCATTACATATGCCCATTGATATTCAATTC
SLH_AL_0106 ATTCATGTTTCTCGTTTTCCTCTGATAANCCCTGTTTCTTCGAGTAAACCCACAAGCAAAGCTCCATTTCCTTANCCTCCTCCCAAACAAACACTCCCANCTTATTGTTTGTTCATCATATGTGCCAATCAATTCTTTGTCCAAGAACCCATATAAAAACCATTACCATATTCATTACATATGCCCATTGATATTCAATTC
SLH_AL_3065 NNNNNNNNNNNNNGTTTTCCTCTGATAANCCCTGTTTCTTCAAGTAAACCCACAAGCAAAGCTCCATTTCCTTANCCTCCTCCCAAACAAACACTCCCANCTTATTGTTTGTTCATCATATGTGCCAATCAATTCTTTGTCCNANAACCNATNTAAAAACCATTACCATATTCATTACGTATGCCCATTCATATTCAATTC
SLH_AL_3066 NTTCATGTTTCTCGTTTTCCTCTGATAANCCCTGTTTCTTCGAGTAAACCCACAAGCAAAGCTCCATTTCCTTANCCTCCTCCCAAACAAACACTCCCANCTTATTGTTTGTTCATCATATGTGCCAATCAATTCTTTGTCCAAGAACCCATATAAAAACCATTACCATATTCATTACATATGCCCATTGATATTCAATTC
// - - * - - - - - - * - - |2:A_tuberculatus_Chr01:101256-101456
assembly_reference_sequence ATGTGTTCAGGTACAATATTTTGATATTTAGGCTTTTAAAGGAAAACCGGCTTAAAGAGGTTTGTGATTTGTTGTTGGATATGAAGGAGAGCCAAATCGTGCCCGATAAGGTGACCATGAATGCTGTATTGTGCTTCTTTTGTAAGGCTGGAATGATGGATGTTGTAGTTGACTTGTATGAAGACAAGGCTGAATTTGGGCTTACTCCACATAGTTTGGTGTTTAATTTTGTTATGAACACTCTATGCGGTGATGGAAGTATTGATG
SLH_AL_0012 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTTAAAGAGGTTTGTGATTTGTTGTTGGATATGAAGGAGANCCAAATCGTGCCCGATAAGGTGACCATGAATGCTGTATTGTGCTTCTTTTGTAAGGCTGGAATGATGGATGTTGTAGTTGACTTGTATGAAGACAAGGCTGAATTTGGGCTTACTCCACATAGTTTGGTGTTTAATTTTGTTATGAACACTCTATGCNGTGATGGAAGTATTGATG
SLH_AL_0014 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTTAAAGAGGTTTGTGATTTGTTGTTGGATATGAAGGAGANCCAAATCGTGCCCGATAAGGTGACCATGAATGCTGTATTGTGCTTCTTTTGTAAGGCTGGAATGATGGATGTTGTAGTTGACTTGTATGAAGACAAGGCTGAATTTGGGCTTACTCCACATAGTTTGGTGTTTAATTTTGTTATGAACACTCTATGCNGTGATGGAAGTATTGATG
SLH_AL_0018 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTTAAAGAGGYTTGTGATTTGTTGTTGGATATGAAGGAGANCCAAATCGTGCCCGATAAGGYGACCATGAATGCTGTATTGTGCTTCTTTTGTAAGGCTGGAATGATGGATGTTGTAGTTGACTTGTATGAAGACAAGGCTGAATTTGGGCTTACTCCACATAGTTTGGTGTTTAATTTTGTTATGAACACTCTATGCNGTGATGGAAGTATTGATG
SLH_AL_0030 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTTAAAGAGGTTTGTGATTTGTTGTTGGATATGAAGGAGANCCAAATCGTGCCCGATAAGGTGACCATGAATGCTGTATTGTGCTTCTTTTGTAAGGCTGGAATGATGGATGTTGTAGTTGACTTGTATGAAGACAAGGCTGAATTTGGGCTTACTCCACATAGTTTGGTGTTTAATTTTGTTATGAACACTCTATGCNGTGATGGAAGTATTGATG
SLH_AL_0034 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTTAAAGAGGTTTGTGATTTGTTGTTGGATATGAAGGAGANCCAAATCGTGCCCGATAAGGTGACCATGAATGCTGTATTGTGCTTCTTTTGTAAGGCTGGAATGATGGATGTTGTAGTTGACTTGTATGAAGACAAGGCTGAATTTGGGCTTACTCCACATAGTTTGGTGTTTAATTTTGTTATGAACACTCTATGCNGTGATGGAAGTATTGATG
SLH_AL_0036 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTTAAAGAGGTTTGTGATTTGTTGTTGGATATGAAGGAGANCCAAATCGTGCCCGATAAGGTGACCATGAATGCTGTATTGTGCTTCTTTTGTAAGGCTGGAATGATGGATGTTGTAGTTGACTTGTATGAAGACAAGGCTGAATTTGGGCTTACTCCACATAGTTTGGTGTTTAATTTTGTTATGAACACTCTATGCNGTGATGGAAGTATTGATG
SLH_AL_0042 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTTAAAGAGGTTTGTGATTTGTTGTTGGATATGAAGGAGANCCAAATCGTGCCCGATAAGGTGACCATGAATGCTGTATTGTGCTTCTTTTGTAAGGCTGGAATGATGGATRTTGTAGTTGACTTGTATGAAGACAAGGCTGAATTTGGGCTTACTCCACATAGTTTGGTGTTTAATTTTGTTATGAACACTCTATGCNGTGATGGAAGTATTGATG
SLH_AL_0048 ATGTGTTCAGGTACAATATTTTGATATTTAGGCTTTTAAAGGAAAACCGGCTTAAAGAGGTTTGTGATTTGTTGTTGGATATGAAGGAGANCCAAATCGTGCCCGATAAGGTGACCATGAATGCTGTATTGTGCTTCTTTTGTAAGGCTGGAATGATGGATGTTGTAGTTGACTTGTATGAAGACAAGGCTGAATTTGGGCTTACTCCACATAGTTTGGTGTTTAATTTTGTTATGAACACTCTATGCNGTGATGGAAGTATTGATG
SLH_AL_0063 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTTAAAGAGGTTTGTGATTTGTTGTTGGATATGAAGGAGANCCAAATCGTGCCCGATAAGGTGACCATGAATGCTGTATTGTGCTTCTTTTGTAAGGCTGGAATGATGGATGTTGTAGTTGACTTGTATGAAGACAAGGCTGAATTTGGGCTTACTCCACATGGTTTGGTGTTTAATTTTGTTATGAACACTCTATGTNGTGATGGAAGTATTGATG
SLH_AL_0064 ATGTGTTCAGGTACAATATTTTGATATTTAGGCTTTTAAAGGAAAACAGGCTTAAAGAGGTTTGTGATTTGTTGTTGGATATGAAGGAGANCCAAATCGTGCCCGATAAGGTGACCATGAATGCTGTATTGTGCTTCTTTTGTAAGGCTGGAATGATGGATGTTGTAGTTGACTTGTATGAAGACAAGGCTGAATTTGGGTTTACTCCACATGGTTTGGTGTTTAATTTTGTTATGAACACTCTATGTNGTGATGGAAGTATTGATG
SLH_AL_0100 ATGTGTTCAGGTACAATATTTTGATATTTAGGCTTTTAAAGGAAAACAGGCTTAAAGAGGTTTGTGATTTGTTGTTGGATATGAAGGAGANCCAAATCGTGCCCGATAAGGTGACCATGAATGCTGTATTGTGCTTCTTTTGTAAGGCTGGAATGATGGATGTTGTAGTTGACTTGTATGAAGACAAGGCTGAATTTGGGTTTACTCCACATGGTTTGGTGTTTAATTTTGTTATGAACACTCTATGTNGTGATGGAAGTATTGATG
SLH_AL_0101 ATGTGTTCAGGTACAATATTTTGATATTTAGGCTTTTAAAGGAAAACAGGCTTAAAGAGGTTTGTGATTTGTTGTTGGATATGAAGGAGANCCAAATCGTGCCCGATAAGGTGACCATGAATGCTGTATTGTGCTTCTTTTGTAAGGCTGGAATGATGGATGTTGTAGTTGACTTGTATGAAGACAAGGCTGAATTTGGGTTTACTCCACATGGTTTGGTGTTTAATTTTGTTATGAACACTCTATGTNGTGATGGAAGTATTGATG
SLH_AL_0104 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTTAAAGAGGTTTGTGATTTGTTGTTTGATATGAAGGAGANCCAAATCGTGCCCGATAAGGTGACCATGAATGCTGTATTGTGCTTCTTTTGTAAGGCTGGAATGATGGATGTTGTAGTTGACTTGTATGAAGACAAGGCTGAATTTGGGCTTACTCCACATGGTTTGGTGTTTAATTTTGTTATGAACACTCTATGCNGTGATGGAAGTATTGATG
SLH_AL_0105 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTTAAAGAGGTTTGTGATTTGTTGTTGGATATGAAGGAGANCCAAATCGTGCCCGATAAGGTGACCATGAATGCTGTATTGTGCTTCTTTTGTAAGGCTGGAATGATGGATGTTGTAGTTGACTTGTATGAAGACAAGGCTGAATTTGGGCTTACTCCACATGGTTTGGTGTTTAATTTTGTTATGAACACTCTATGTNGTGATGGAAGTATTGATG
SLH_AL_0106 ATGTGTTCAGGTACAATATTTTGATATTTAGGCTTTTAAAGGAAAACAGGCTTAAAGAGGTTTGTGATTTGTTGTTGGATATGAAGGAGANCCAAATCGTGCCCGATAAGGTGACCATGAATGCTGTATTGTGCTTCTTTTGTAAGGCTGGAATGATGGATGTTGTAGTTGACTTGTATGAAGACAAGGCTGAATTTGGGTTTACTCCACATGGTTTGGTGTTTAATTTTGTTATGAACACTCTATGTNGTGATGGAAGTATTGATG
SLH_AL_3065 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTTAAAGAGGTTTGTGATYTGTTGTTTGATATGAAGGAGANCCAAATCGTGCCCGATAAGGTGACCATGAATGCTGTATTGTGCTTCTTTTGTAAGGCTGGAATGATGGATGTTGTAGTTGACTTGTATGAAGACAAGGCTGAATTTGGGCTTACTCCACATGGTTTGGTGTTTAATTTTGTTATGAACACTCTATGCNGTGATGGAAGTATTGATG
SLH_AL_3066 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTTAAAGAGGTTTGTGATTTGTTGTTGGATATGAAGGAGANCCAAATCGTGCCCGATAAGGTGACCATGAATGCTGTATTGTGCTTCTTTTGTAAGGCTGGAATGATGGATGTTGTAGTTGACTTGTATGAAGACAAGGCTGAATTTGGGCTTACTCCACATGGTTTGGTGTTTAATTTTGTTATGAACACTCTATGTNGTGATGGAAGTATTGATG
// * - - * - - * * * |3:A_tuberculatus_Chr01:102530-102796
assembly_reference_sequence AAGTATGATGAGGCTGTGCTATTAATCAAAGAAATGGAGAAAGTGGGGCGTTCGATTTCATCGTTTGTTGGTAATACACTTTTGTTGAACTCACTTTATAATGACAACTTGCACAAGGCTTGGCTTCGTTTGAGAGATCCATCTAATGAAACACCTAGAAGTGCAATGCTTGGCCAGGTTATTGCTGTTTTTTCTGGCCAAATAAATAGTGATGTTAAGGCGGAGGACTTGGAAGAACTTGTTCAAGAATGCTTTCCACTTGATCTCTACTCTTACAACATGATAATGAGAAAATTGAGCATCAATAACATCGATG
21040XD-01-08_S40_L002 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTTTATAATGACAACTTGCAGAAGGCTTGGCTTCGTTTGAGAGATCCATCTAATGAAACACCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
SLH_AL_0012 AAGTATGATGAGGCTGTGCTATTAATCAAAGAAATGGAGAAAGTTGGGCGTTCGATTTCATCGTTTGTTGGTAATACACTTTTGTTGAACTCACTTTATAATGACAACTTGCACAAGGCTTGGCTTCGTTTGAGAGATCCATCTAATGAAACACCTAGNAGTGCAATGCTTGGCCAGGNTATTGCTGTTTTTTCTGGCCAAATAAATAGTGATGTTAAGGCGGAGGACTTGGAAGAACTTGTTCAAGAATGCTTTCCACTTGATCTCTANTCTTACAACATGATAATGAGAAAATTGAGCATCAATAACATCGANG
SLH_AL_0014 AAGTATGATGAGGCTGTGCTATTAATCAAAGAAATGGAGAAAGTTGGGCGTTCGATTTCATCGTTTGTTGGTAATACACTTTTGTTGAACTCACTTTATAATGACAACTTGCACAAGGCTTGGCTTCGTTTGAGAGATCCATCTAATGAAACACCTAGNAGTGCAATGCTTGGCCAGGNTATTGCTGTTTTTTCTGGCCAAATAAATAGTGATGTTAAGGCGGAGGACTTGGAAGAACTTGTTCAAGAATGCTTTCCACTTGATCTCTANTCTTACAACATGATAATGAGAAAATTGAGCATCAATAACATCGANG
SLH_AL_0018 AAGTATGATGAGGCTGTGCTATTAATCAAAGAAATGGAGAAAGTTGGGCGTTCGATTTCATCGTTTGTTGGTAATACACTTTTGTTGAACTCACTTTATAATGACAACTTGCACAAGGCTTGGCTTCGTTTGAGAGATCCATCTAATGAAACACCTAGNAGTGCAATGCTTGGCCAGGNTATTGCTGTTTTTTCTGGCCAAATAAATAGTGATGTTAAGGCGGAGGACTTGGAAGAACTTGTTCAAGAATGCTTTCCACTTGATCTCTANTCTTACAACATGATAATGAGAAAATTGAGCATCAATAACATCGANG
SLH_AL_0030 AAGTATGATGAGGCTGTGCTATTAATCAAAGAAATGGAGAAAGTTGGGCGTTCGATTTCATCGTTTGTTGGTAATACACTTTTGTTGAACTCACTTTATAATGACAACTTGCACAAGGCTTGGCTTCGTTTGAGAGATCCATCTAATGAAACACCTAGNAGTGCAATGCTTGGCCAGGNTATTGCTGTTTTTTCTGGCCAAATAAATAGTGATGTTAAGGCGGAGGACTTGGAAGAACTTGTTCAAGAATGCTTTCCACTTGATCTCTANTCTTACAACATGATAATGAGAAAATTGAGCATCAATAACATCGANG
SLH_AL_0036 AAGTATGATGAGGCTGTGCTATTAATCAAAGAAATGGAGAAAGTTGGGCGTTCGATTTCATCGTTTGTTGGTAATACACTTTTGTTGAACTCACTTTATAATGACAACTTGCACAAGGCTTGGCTTCGTTTGAGAGATCCATCTAATGAAACACCTAGNAGTGCAATGCTTGGCCAGGNTATTGCTGTTTTTTCTGGCCAAATAAATAGTGATGTTAMGGCGGAGGACTTGGAAGAACTTGTTCAAGAATGCTTTCCACTTGATCTCTANTCTTACAACATGATAATGAGAAAATTGAGCATCAATAACATCGANG
SLH_AL_0042 AAGTATGATGAGGCTGTGCTATTAATCAAAGAAATGGAGAAAGTTGGGCGTTCGATTTCATCGTTTGTTGGTAATACACTTTTGTTGAACTCACTTTATAATGACAACTTGCACAAGGCTTGGCTTCGTTTGAGAGATCCATCTAATGAAACACCTAGNAGTGCAATGCTTGGCCAGGNTATTGCTGTTTTTTCTGGCCAAATAAATAGTGATGTTAAGGCGGAGGACTTGGAAGAACTTGTTCAAGAATGCTTTCCACTTGATCTCTANTCTTACAACATGATAATGAGAAAATTGAGCATCAATAACATCGANG
SLH_AL_0048 AAGTATGATGAGGCTGTGCTATTAATCAAAGAAATGGAGAAAGTKGGGCGTTCGATTTCATCGTTTGTTGGTAATACACTTTTGTTGAACTCACTTTATAATGACAACTTGCACAAGGCTTGGCTTCGTTTGAGAGATCCATCTAATGAAACACCTAGNAGTGCAATGCTTGGCCAGGNTATTGCTGTTTTTTCTGGCCAAATAAATAGTGATGTTAAGGCGGAGGACTTGGAAGAACTTGTTCAAGAATGCTTTCCACTTGATCTCTANTCTTACAACATGATAATGAGAAAATTGAGCATCAATAACATCGANG
SLH_AL_0063 AAGTATGATGAGGCTGTGCTATTAATCAAAGAAATGGAGAAAGTTGGGCGTTCGATTTCATCTTTTGTTGGTAATACACTTTTGTTGAACTCACTTTATAATGACAACTTGCAGAAGGCTTGGCTTCGTTTGAGAGATCCATCTAATGAAACACCTAGNAGTGCAATGCTTGGCCAGGNTATTGCTGTTTTTTCTGGCCAAATAAATAGTGATGTTAAGGCGGAGGACATGGAAGAACTTGTTCAAAAATGCTTTCCACTTGATCTGTANTCTTACAACATGATTATGAGAAAATTGAGCATCAATAACGTCGANG
SLH_AL_0064 AAGTATGATGAGGCTGTGCTATTAATCAAAGAAATGGAGAAAGTTGGGCGTTCGATTTCATCTTTTGTTGGTAATACACTTTTGTTGAACTCACTTTATGATGACAACTTGCAGAAGGCTTGGCTTCGTTTGAGAGATCCATCTAATGAAACACCTAGNAGTGCAATGCTTGGCCAGGNTATTGCTGTTTTTTCTGGCCAAATAAATAGTGATGTTAAGGCGGAGGACATGGAAGAACTTGTTCAAAAATGCTTTCCACTTGATCTGTANTCTTACAACATGATTATGAGAAAATTGAGCATCAATAACATCGANG
SLH_AL_0100 AAGTATGATGAGGCTGTGCTATTAATCAAAGAAATGGAGAAAGTTGGGCGTTCGATTTCATCTTTTGTTGGTAATACACTTTTGTTGAACTCACTTTATGATGACAACTTGCAGAAGGCTTGGCTTCGTTTGAGAGATCCATCTAATGAAACACCTAGNAGTGCAATGCTTGGCCAGGNTATTGCTGTTTTTTCTGGCCAAATAAATAGTGATGTTAAGGCGGAGGACATGGAAGAACTTGTTCAAAAATGCTTTCCACTTGATCTGTANTCTTACAACATGATTATGAGAAAATTGAGCATCAATAACATCGANG
SLH_AL_0101 AAGTATGATGAGGCTGTGCTATTAATCAAAGAAATGGAGAAAGTTGGGCGTTCGATTTCATCTTTTGTTGGTAATACACTTTTGTTGAACTCACTTTATGATGACAACTTGCAGAAGGCTTGGCTTCGTTTGAGAGATCCATCTAATGAAACACCTAGNAGTGCAATGCTTGGCCAGGNTATTGCTGTTTTTTCTGGCCAAATAAATAGTGATGTTAAGGCGGAGGACATGGAAGAACTTGTTCAAAAATGCTTTCCACTTGATCTGTANTCTTACAACATGATTATGAGAAAATTGAGCATCAATAACATCGANG
SLH_AL_0105 AAGTATGATGAGGCTGTGCTATTAATCAAAGAAATGGAGAAAGTTGGGCGTTCGATTTCATCTTTTGTTGGTAATACACTTTTGTTGAACTCACTTTATAATGACAACTTGCAGAAGGCTTGGCTTCGTTTGAGAGATCCATCTAATGAAACACCTAGNAGTGCAATGCTTGGCCAGGNTATTGCTGTTTTTTCTGGCCAAATAAATAGTGATGTTAAGGCGGAGGACATGGAAGAACTTGTTCAAAAATGCTTTCCACCTGATCTGTANTCTTACAACATGATTATGAGAAAATTGAGCATCAATAACATCGANG
SLH_AL_0106 AAGTATGATGAGGCTGTGCTATTAATCAAAGAAATGGAGAAAGTTGGGCGTTCGATTTCATCTTTTGTTGGTAATACACTTTTGTTGAACTCACTTTATGATGACAACTTGCAGAAGGCTTGGCTTCGTTTGAGAGATCCATCTAATGAAACACCTAGNAGTGCAATGCTTGGCCAGGNTATTGCTGTTTTTTCTGGCCAAATAAATAGTGATGTTAAGGCGGAGGACATGGAAGAACTTGTTCAAAAATGCTTTCCACTTGATCTGTANTCTTACAACATGATTATGAGAAAATTGAGCATCAATAACATCGANG
SLH_AL_3066 AAGTATGATGAGGCTGTGCTATTAATCAAAGAAATGGAGAAAGTTGGGCGTTCGATTTCATCTTTTGTTGGTAATACACTTTTGTTGAACTCACTTTATAATGACAACTTGCAGAAGGCTTGGCTTCGTTTGAGAGATCCATCTAATGAAACACCTAGNAGTGCAATGCTTGGCCAGGNTATTGCTGTTTTTTCTGGCCAAATAAATAGTGATGTTAAGGCGGAGGACATGGAAGAACTTGTTCAAAAATGCTTTCCACCTGATCTGTANTCTTACAACATGATTATGAGAAAATTGAGCATCAATAACATCGANG
// * * * * - * * * * * - |4:A_tuberculatus_Chr01:103624-103939
assembly_reference_sequence GTGGTGAGAAAGAAAGGATCCTAGTCTTATGATATCCTACATGGCATCATACTATTAATACACAAAACCTCTCTTGTCCAAGTAATTATCTGACTCAGCAAATCTATCAACACCAACTATTCTGTTCATGTCACTTTCAGTTGTGATCAAGTTATAAATTCACTTTTTAATTTGA
21040XD-01-07_S39_L002 GTGGTGNNAAAGAAAGGATCCTAGTCTTATGNTATCCTACATGGCATCATANTATNNATACACNAAANCTCTCTTGTCCAAGTAATTATCTGACTNNNNNNNNNNNNNNNNNNNAACTANTNTGTTNATGTCACTTTCANTTGTGNTCAAGTNATAAATTCACTTTTNNNNNNNN
SLH_AL_0014 GTGGTGAGAAAGAAAGGATCCTAGTCTTATGRTATCCTACATGGCATCATACTATTAATACACAAAACCTCTCTTGTCCAAGTAATTATCTGACTCAGCAAATCTATCAACACCAACTAATCTGTTCATGTCACTTTCAGTTGTGATCAAGTTATAAATTCACTTTTTAWTTTGA
SLH_AL_0034 GTGGTGAGAAAGAAAGGATCCTAGTCTTATGGTATCCTACATGGCATCATACTATTAATACACCAAACCTCTCTTGTCCAAGTAATTATCTGACTCAGCAAATCTATCWACACCAACTAATCTGTTCATGTCACTTTCAGTTGTGATCAAGTTATAAATTCACTTTTTATTTTGA
SLH_AL_0042 GTGGTGAGAAAGAAAGGATCCTAGTCTTATGGTATCCTACATGGCATCATACTATTAATACACAAAACCTCTCTTGTCCAAGTAATTATCTGACTCAGCAAATCTATCAACACCAACTAATCTGTTCATGTCACTTTCAGTTGTGATCAAGTTATAAATTCACTTTTTATTTTGA
SLH_AL_0104 GTGGTGGGAAAGAAAGGATCCTAGTCTTATGGTATCCTACATGGCATCATANTATTGATACACAAAACCTCTCTTGTCCAAGTAATTATCTGACTCAGCAAATCTNTCAACACCAACTAATTTGTTTATGTCACTTTCAATTGTGTTCAAGTCATAAATTCACTTTTTATTTTGA
SLH_AL_0105 GTGGTGGGAAAGAAAGGATCCTAGTCTTATGGTATCCTACATGGCATCATANTATTAATACACAAAAGCTCTCTTGTCCAAGTAATTATCTGACTCAGCAAATCTNTCNACACCAACTAATTTGTTCATGTCACTTTCAATTGTGTTCAAGTCATAAATTCACTTTTTANNNNNN
// * * - - - - - * - * * * * |5:A_tuberculatus_Chr01:110679-110853
assembly_reference_sequence CTAGAGAGAGAAAGTGATGATGATGATGAAGGAAGTGATCACTAACACCACAAAAACAAACAACACAATGTCAATGGTAGATGGAAGTGTAGTTCAACAAGGATGGAAAACACCAATACCATATCTCTTTGGTGGACTTGCACTTATGCTATGTCTTATTGCTATTGCTTTGCTTATTCTTGCTTGTTCTTTTAGAAAATCTCATCACAACAACAACAACAACAACAATGGAAACGGAAAACCGAAAACCGATTTTTCCAACAAAGGAAGTCAAAACGACATGAAAATTGTCGTAATTATGG
21040XD-01-07_S39_L002 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCAACANNAATGGAAANNNNAAACCNAAAACNGANNTTNNCNACAAANNAANTCAAANCGACNTNAAANTNGTCGTAATTATGG
SLH_AL_0012 CTAGAGAGAGAAAG---TGATGATGATGAAGGAAGTAATCACTAACACCACAAAAACAAACAACACAATGTCAATGGTAAATGGAAGT---GTTCAACAAGGATGGAAAACACCAATACCATATCTCTTTGGTGGACTTGCACTTATGCTNTGTCTTATTGCTATTGCTTTGCTTATTCTTGCTTGTTCTTTTAGAAAATCTCATC------ACAACAACAACAACAATGGAAACGGAAAACCAAAAACCGATTTTTCCAACAAAGGAAGTCAAANCGACATGAAANTTGTCGTAATTATGG
SLH_AL_0014 CTAGAGAGAGAAAG---TGATGATGATGAAGGAAGTRATCACTAACACCACAAAAACAAACAACACAATGTCAATGGTAAATGGAAGT---GTTCAACAAGGATGGAAAACACCAATACCATATCTCTTTGGTGGACTTGCACTTATGCTNTGTCTTATTGCTATTRCTTTGCTTATTCTWGCTTGTTCTTTTASAAAATCTCATCACA---ACAACAACAACAACAATGGAAACGGAAAACCAAAAACCGATTTTTCCAACAAAGGAAGTCAAANCGACATGAAANTTGTCGTAATTATGG
SLH_AL_0018 CTAGAGAGNGAAAG---TGATGATGATGAAGGAAGTGATCACTAACACCACAAAAACAAACAACACAATGTCAATGGTANATGGAAGTGTAGTTCAACAAGGATGGAAAACACCAATACCATATCTCTTTGGTGGACTTGCACTTATGCTNTGTCTTATTGCTATTGCTTTGCTTATTCTNGCTTGTTCTTTTAGAAAATCTCATC------ACAACAACAACAACAATGGAAACGGAAAACCNAAAACCGATTTTTCCAACAAAGGAAGTCAAANCGACATGAAANTTGTCGTAATTATGG
SLH_AL_0030 CTAGAGAGAGAAAG---TGATGATGATGAAGGAAGTGATCACTAACACCACAAAAACAAACAACACAATGTCAATGGTAGATGGAAGT---GTTCAACAAGGATGGAAAACACCAATACCATATCTCTTTGGTGGACTTGCACTTATGCTNTGTCTTATTGCTATTGCTTTGCTTATTCTNGCTTGTTCTTTTAGAAAATCTCATCACA---ACAACAACAACAAYAATGGAAACGGAAAACCAAAAACCGATTTTTCCNACAAAGGAAGTCAAANCGACATGAAANTTGTCGTAATTATGG
SLH_AL_0034 CTAGAGAGAGAAAG---TGATGATGATGAAGGAAGTGATCACTAACACCACAAAAACAAACAACACAATGTCAATGGTARATGGAAGT---GTTCAACAAGGATGGAAAACACCAATACCATATCTCTTTGGTGGACTTGCACTTATGCTNTGTCTTATTGCTATTGCTTTGCTTATTCTWGCTTGTTCTTTTAGAAAATCTCATCACA---ACAACAACAACAACAATGGAAACGGAAAACCRAAAACCGATTTTTCCAACAAAGGAAGTCAAANCGACWTGAAANTTGTCGTAATTATGG
SLH_AL_0048 CTAGAGAGAGAAAG---TGATGATGATGAAGGAAGTNATCACTAACACCACAAAAACAAACAACACAATGTCAATGGTANATGGAAGT---GTTCAACAAGGATGGAAAACACCAATACCATATCTCTTTGGTGGACTTGCACTTATGCTNTGTCTTATTGCTATTGCTTTGCTTATTCTNGCTTGTTCTTTTAGAAAATCTCATC------ACAACAACAACAACAATGGAAACGGAAAACCAAAAACCGATTTTTCCAACAAAGGAAGTCAAANCGACATGAAANTTGTCGTAATTATGG
SLH_AL_0063 NTAGAGAGAGAAANTGATGATGATGATGAAGGAAGTGATCACT---------------AACAACACAATGTCAATGGTAGATGGAAGNGTAGTTNAACAAGGATGGAAAACACCAATACCATATCTCTTTGGTGGACTTGCACTTATGCTATGTCTTATTGCTATTGCTTTGCTTATTCTTGCTTCTTCTTTTACAAAATCTCATNACAACAACAACAACAACAACAATGGAAACCCAAAACCAAAAACGGATTTTTCCAACAAACAAACTCAAANCGACATGAAANTCGTCGTAATTATGG
SLH_AL_0064 NTAGAGAGAGAAANTGATGATGATGATGAAGGAAGTGATCACTAACACCACAAAAACAAACAACACAATGTCAATGGTAGATGAAAGNGTAGTTNAACAAGGATGGAAAACACCAATACCATATCTCTTTGGTGGACTTGCACTTATGCTNTGTCTTATTGCTATTGCTTTGCTTATTCTTGCTTGTTCTTTTACAAAATCTCATNACAACAACAACACCAACAACAATGGAAACCCAAAACCTAAAACGGATTTTTCCAACAAAGAAACTCAAANCGACATGAAANTCGTCGTAATTATGG
SLH_AL_0084 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNACTAACACCACAAAAACAAACAACACAATGTCAATGGTAGATGGAAGT---GTTNAACAAGGATGGAAAACACCAATACCATATCTCTTTGGTGGACTTGCACTTATGCTATGTCTTATTGCTATTGCTTTGCTTATTCTTGCTTGTTCTTTTACTAAATCTCATNACAACAACAACNNCAACAACAATGGAAACCCAAAACCAAAAACGGATNTTTNCAACAAAGGAACTCAAANCGACATNAAANTTGTCGTAATTATGG
SLH_AL_0100 NTAGAGAGAGAAANTGATGATGATGATGAAGGAAGTGATCACTAACACCACAAAAACAAACAACACAATGTCAATGGTAGATGAAAGNGTAGTTNAACAAGGATGGAAAACACCAATACCATATCTCTTTGGTGGACTTGCACTTATGCTNTGTCTTATTGCTATTGCTTTGCTTATTCTTGCTTGTTCTTTTACAAAATCTCATNACAACAACAACACCAACAACAATGGAAACCCAAAACCTAAAACGGATTTTTCCAACAAAGAAACTCAAANCGACATGAAANTCGTCGTAATTATGG
SLH_AL_0101 NTAGAGAGAGAAANTGATGATGATGATGAAGGAAGTGATCACTAACACCACAAAAACAAACAACACAATGTCAATGGTAGATGAAAGNGTAGTTNAACAAGGATGGAAAACACCAATACCATATCTCTTTGGTGGACTTGCACTTATGCTNTGTCTTATTGCTATTGCTTTGCTTATTCTTGCTTGTTCTTTTACAAAATCTCATNACAACAACAACACCAACAACAATGGAAACCCAAAACCTAAAACGGATTTTTCCAACAAAGAAACTCAAANCGACATGAAANTCGTCGTAATTATGG
SLH_AL_0104 CTAGAGAGAGAAAGTGATGATGATGATGAAGGAAGTGATGASTAACACCACAAAAACAAACAACACAATGTCAATGGTAGATGGAAGT---GTTNAACAAGGATGGAAAACACCAATACCATATCTCTTTGGTGGACTTGCACTTATGCTNTGTCTTATTGCTATTGCTTTGCTTATTCTTGCTTGTTCTTTTACWAAATCTCATNACAACAACAACMACAACAACAATGGAAACCCWAAACCAAAAACGGATCTTTCCAACAAAGGAASTCAAANCGACATSAAANTTGTCGTAATTATGG
SLH_AL_0105 NTAGAGAGAGAAANTGATGATGATGATGAAGGAAGTGATCACT---------------AACAACACAATGTCAATGGTAGATGGAAGNGTAGTTNAACAAGGATGGAAAACACCAATACCATATCTCTTTGGTGGACTTGCACTTATGCTATGTCTTATTGCTATTGCTTTGCTTATTCTTGCTTCTTCTTTTACAAAATCTCATNACAACAACAACAACAACAACAATGGAAACCCAAAACCAAAAACGGATTTTTCCAACAAACAAACTCAAANCGACATGAAANTCGTCGTAATTATGG
SLH_AL_0106 NTAGAGAGAGAAANTGATGATGATGATGAAGGAAGTGATCACTAACACCACAAAAACAAACAACACAATGTCAATGGTAGATGAAAGNGTAGTTNAACAAGGATGGAAAACACCAATACCATATCTCTTTGGTGGACTTGCACTTATGCTNTGTCTTATTGCTATTGCTTTGCTTATTCTTGCTTGTTCTTTTACAAAATCTCATNACAACAACAACACCAACAACAATGGAAACCCAAAACCTAAAACGGATTTTTCCAACAAAGAAACTCAAANCGACATGAAANTCGTCGTAATTATGG
SLH_AL_3066 NTAGAGAGAGAAANTGATGATGATGATGAAGGAAGTGATCACT---------------AACAACACAATGTCAATGGTAGATGGAAGNGTAGTTNAACAAGGATGGAAAACACCAATACCATATCTCTTTGGTGGACTTGCACTTATGCTATGTCTTATTGCTATTGCTTTGCTTATTCTTGCTTCTTCTTTTACAAAATCTCATNACAACAACAACAACAACAACAATGGAAACCCAAAACCAAAAACGGATTTTTCCAACAAACAAACTCAAANCGACATGAAANTCGTCGTAATTATGG
// * - - * * - * * ** -* - **- * * - ** * - - * |6:A_tuberculatus_Chr01:116394-116695
assembly_reference_sequence CTTTTCCTCTTAATTATTAGTTTTCGAAGTACATAATGAGTGATCACTAAGTCAGCACTAACAAGTTATTGGCATATCTTCATAAATATAACCCTATTTGGACTATAACTTATATTTTAAAGTGCTTTTATATATTGAGTATATAATTTTGTACATGATATGTGTTAATGATTGCTAGCTTAAGTCATTTAACTAAAATAGAACAATGCATATACCATTACAGGAAGGGTTAGCCATACGATATTTA
21040XD-01-08_S40_L002 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCNTAATGAGTGATCACTAAGTNANCACTAACAANTTATTGGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTATNACTTATNTTTTNAAGTGNTTTTATATATTNAGTATATNATTTTNTANANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTANAACAATNCATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
SLH_AL_0063 CTTTTCCTCTTAATTATTAGTATTCGANGTACATAATGAGTGATCACTAAGTCACCACTAACAAGTTATTGGCATATCTTNATAAATATAACCCTATTTGGACTATAACTTATATTTTAAAGTGNTTTTATATATTGAGTATATAATTTTGTANATGATATGTGTTAATGATTGCTAGCTTAAATCATTTAACTAAAATAGAACAATCCATATACCATTACATGAAGGGTTAGCCATACAATATTTA
SLH_AL_0064 CTTTTCCTCTTAATTATTAGTATTCGANGTACATAATGAGTGATCACTAAGTCACCACTAACAAGTTATTGGCATATCTTNATAAATATAACCCTATTTGGACTATAACTTATATTTTGAAGTGNTTTTATATATTGAGTATATAATTTTGTANATGATATGTGTTAATGATTGCTAGCTTAAATCATTTAACTAAAATAAAACAATCCATATACGATTACATGAAGGGTTAGCCATACAATATTTA
SLH_AL_0100 CTTTTCCTCTTAATTATTAGTATTCGANGTACATAATGAGTGATCACTAAGTCACCACTAACAAGTTATTGGCATATCTTNATAAATATAACCCTATTTGGACTATAACTTATATTTTGAAGTGCTTTTATATATTGAGTATATAATTTTGTANATGATATGTGTTAATGATTGCTAGCTTAAATCATTTAACTAAAATAAAACAATCCATATACGATTACATGAAGGGTTAGCCATACAATATTTA
SLH_AL_0101 CTTTTCCTCTTAATTATTAGTATTCGANGTACATAATGAGTGATCACTAAGTCACCACTAACAAGTTATTGGCATATCTTNATAAATATAACCCTATTTGGACTATAACTTATNTTTTGAAGTGNTTTTATATATTGAGTATATAATTTTGTANATGATATGTGTTAATGATTGCTAGCTTAAATCATTTAACTAAAATAAAACAATCCATATACGATTACATGAAGGGTTAGCCATACAATATTTA
SLH_AL_0105 CTTTTCCTCTTAATTATTAGTATTCGANGTACATAATGAGTGATCACTAAGTCACCACTAACAAGTTATTGGCATATCTTNATAAATATAACCCTATTTGGACTATAACTTATATTTTAAAGTGCTTTTATATATTGAGTATATAATTTTGTAC-TGATATGTGTTAATGATTGCTAGCTTAAATCATTTAACTAAAATAGAACAATCCATATACCATTACATGAAGGGTTAGCCATACAATATTTA
SLH_AL_0106 CTTTTCCTCTTAATTATTAGTATTCGANGTACATAATGAGTGATCACTAAGTCACCACTAACAAGTTATTGGCATATCTTNATAAATATAACCCTATTTGGACTATAACTTATATTTTGAAGTGNTTTTATATATTGAGTATATAATTTTGTANATGATATGTGTTAATGATTGCTAGCTTAAATCATTTAACTAAAATAAAACAATCCATATACGATTACATGAAGGGTTAGCCATACAATATTTA
SLH_AL_3066 CTTTTCCTCTTAATTATTAGTATTCGANGTACATAATGAGTGATCACTAAGTCACCACTAACAAGTTATTGGCATATCTTNATAAATATAACCCTATTTGGACTATAACTTATATTTTAAAGTGNTTTTATATATTGAGTATATAATTTTGTANATGATATGTGTTAATGATTGCTAGCTTAAATCATTTAACTAAAATAGAACAATCCATATACGATTACATGAAGGGTTAGCCATACAATATTTA
// - - * - * - * - - |7:A_tuberculatus_Chr01:164410-164656
assembly_reference_sequence TTAGAGAGATAAACATGGAGATTTTTGTAAATAGAAAAAAGATGGGTTTTTTTGTTGGGGAAGACCAAATTTTGATTATTGTGGAAAATTAGGCAAAATTTAGGGAAAATATGGAAAGAGAGAAGCGTACGTGGAAAGAAGTAGAAGAAAATGAAGTCAGAAATTAGAATAGTAGTACAAGAATATTAGATAAATTAACAGGGTTT
SLH_AL_0012 TTAGAGAGATAAACATGGAGATTTTTGTAAATAGAAAAAAGATGGGTTTTTTTGTTGGGGAAGACCAAATTTTGATTATTGTGGAAAATTAGGCAAAATTTAGGGAAAATATGGAAAGAGAGAAGCGTACGTGGAAAGAWGTAGAAGAAAATGAAGTCAGAAATTAGAATAGTAGTACAANAANATTAGATAAATTAACAGGGTTT
SLH_AL_0014 TTAGAGAGATAAACATGGAGATTTTTGTAAWTAGAAAANAGATGGG--TTTTTGTTGGGGAAGACCAAATTTTGATTATTGTGGAAAATTAGGCAAAATTTAGGGAAAATATGGAAAGAGAGAARCGTACGTGGAAAGAWGTAGAAGAWAATGAAGTCAGAAATTAGAATAGTAGTTCAANAATATTAGATAAATWAACAGGGTTT
SLH_AL_0018 TTAGAGAGATAAACATGGAGATTTTTGTAAATAGAAAAAAGATGGGTTTTTTTGTTGGGGAAGACCAAATTTTGATTATTGTGGAAAATTAGGCAAAATTTAGGGAAAATATGGAAAGAGAGAAGCGTRCGTGGAAAGATGTAGAAGATAATGAAGTCAGAAATTAGAATAGTANNNNAANAATATTAGATAAATTAACAGGGTTT
SLH_AL_0030 TTAGAGAGATAAACATGGAGATTTTTGTAAATAGAAAAAAGATGGGTTTTTTTGTTGGGGAAGACCAAATTTTGATTATTGTGGAAAATTAGGCAAAATTTAGGGAAAATATGGAAAGAGAGAAGCGTACGTGGAAWGAWGTAGAAGAWAATGAAGTCAGAAATTAGAATAGTAGTACAANAATATTAGATAAATTAACAGGGTTT
SLH_AL_0034 TTAGAGAGATAANCATGGAGATNTTTGTAANTAGAAAANAGATGGNTTTTTTTGTNGGGNAAGACNAAATTTNGANTATTGTGGAAAATTAGGCAAAATTTAGGGAAAATATGGAAAGAGAGAAGCGTACGTGGAAAGAWGTAGAAGAWAATGAAGTCAGAAATTAGAATAGTANNNNAANAANATTRGATAAATTAACAGGGTTT
SLH_AL_0036 TTAGAGAGATAAACATGGAGATTTTTGTAAATAGAAAAAAGATGGGTTTTTTTGTTGGGGAAGACCAAATTTTGATTATTGTGGAAAATTAGGCAAAATTTAGGGAAAATATGGAAAGAGAGAAGCGTACGTGGAAAGATGTAGAAGATAATGAAGTCAGAAATTAGAATAGTANTNNAANAATATTAGATAAATTAACAGGGTTT
SLH_AL_0042 TTAGAGAGATAAACATGGAGATTTTTGTAATTAGAAAANAGATGGG--TTTTTGTTGGGGAAGACCAAATTTTGATTATTGTGGAAAATTAGGCAAAATTTAGGGAAAATATGGAAAGAGAGAAACGTACGTGGAANGAAGTAGAAGAAAATGAAGTCAGAAATTAGAATAGTANTNNAANAATATTAGATAAATTAACAGGGTTT
SLH_AL_0048 TTAGAGAGATAAACATGGAGATTTTTGTAAATAGAAAAAAGATGGGTTTTTTTGTTGGGGAAGACCAAATTTTGATTATWKTGKRRAATTAGGCAAAATTTAGGGAAAATATGGAAAGAGANAAGCGTACGTGGAAAGAWGTAGAAGNNAATGAAGTCAGAAATTAGAATAGTANNNNAANAATATTAGATAAATTAACAGGGTTT
SLH_AL_0063 TTAGAGAGATAAACATGGAGATTTTTGTAAATAGAAAAAAGATGGNTTTTTTTGTTGGGGAAGACCAAATTTAGATTATTGTGGAAAATTAGGCAAAATTTGGAGAAAATATGGAAAGAGAGAAGCGTATGTGGAAAGAAGTAGACGAGAATGAAGTCAGAAATTCGAATAGTAGTAGATNAATATTAGATAAATTAACAGGGTTT
SLH_AL_0064 TTAGAGAGATAAACATGGAGATTTTTGTAAATAGAAAATAGATGGNTTTTTTTGTGGGGGAAGACAAAATTTTGATTATTGTGGAAAATTAGGCAAAATTTAGGGAAAATATGGANAGAGAGAAGCGTACGTGGAAAGAAGTAGAAGGAAATGAAGTCAGAAATTAGAATAGTACTAGAANAATATTAGATAAATTAACAGGGTTT
SLH_AL_0084 TTAGAGAGATAAACATGGAGATTTTTGTAAATAGAAAAAAGATGGGT-TTTTTGTTGGGKAAGACMAAATTTTGATTATTGTGGAAAATTAGGCAAAATTTAGRGAAAAWATGGANAGAGAGAAGCGTACGTGGAAAGAAGTAGAAGRAAATGAMGTCAGAAATTAGAATAGTASTASAANAATATTAGATAAATTAACAGGGTTT
SLH_AL_0100 TTAGAGAGATAAACATGGAGATTTTTGTAAATAGAAAATAGATGGNTTTTTTTGTGGGGGAAGACAAAATTTTGATTATTGTGGAAAATTAGGCAAAATTTAGGGAAAATATGGANAGAGAGAAGCGTACGTGGAAAGAAGTAGAAGGAAATGAAGTCAGAAATTAGAATAGTACTAGAANAATATTAGATAAATTAACAGGGTTT
SLH_AL_0101 TTAGAGAGATAAACATGGAGATTTTTGTAAATAGAAAATAGATGGNTTTTTTTGTGGGGGAAGACAAAATTTTGATTATTGTGGAAAATTAGGCAAAATTTAGGGAAAATATGGANAGAGAGAAGCGTACGTGGAAAGAAGTAGAAGGAAATGAAGTCAGAAATTAGAATAGTACTAGAANAATATTAGATAAATTAACAGGGTTT
SLH_AL_0104 TTAGAGAGATAAACATGGAGATTTTTGTAAATAGAAAAAAGATGGGTTTTTTTGTTGGGGAAGACCAAATTTTGAT------------TTAGGCAAAATTTAGAGAAAAAATGGAAAGAGAGAAGCGTACGTGGAAAGAAGTAGAAGAAAATGACGTCAGAAATTAGAATAGTAGTAGAANAATATTAGATAWATTAACAGGGTTT
SLH_AL_0105 TTAGAGAGATAAACATGGAGATTTTTGTAAATAGAAAAAAGATGGNTTTTTTTGTTGGGGAAGACCAAATTTAGATTATTGTGGAAAATTAGGCAAAATTTGGAGAAAATATGGAAAGAGAGAAGCGTATGTGGAAAGAAGTAGACGAGAATGAAGTCAGAAATTCGAATAGTAGTAGATNAATATTAGATAAATTAACAGGGTTT
SLH_AL_0106 TTAGAGAGATAAACATGGAGATTTTTGTAAATAGAAAATAGATGGNTTTTTTTGTGGGGGAAGACAAAATTTTGATTATTGTGGAAAATTAGGCAAAATTTAGGGAAAATATGGANAGAGAGAAGCGTACGTGGAAAGAAGTAGAAGGAAATGAAGTCAGAAATTAGAATAGTACTAGAANAATATTAGATAAATTAACAGGGTTT
SLH_AL_3065 TTAGAGAGATAAACATGGAGATTTTTGTAAATAGAAAAAAGATGGGTTTTTTTGTTGGGGAAGACCAAATTTTGATTATTGTGGAAAATTAGGCAAAATTTAGAGAAAAAATGGAAAGAGAGAAGCGTNCGTGGAAAGAAGTAGAAGAAAATGACGTCAGAAATTAGAATAGTAGTNNANNAANATTAGATAAATTAACAGGGTTT
SLH_AL_3066 TTAGAGAGATAAACATGGAGATTTTTGTAAATAGAAAAAAGATGGNTTTTTTTGTTGGGGAAGACCAAATTTAGATTATTGTGGAAAATTAGGCAAAATTTGGAGAAAATATGGAAAGAGAGAAGCGTACGTGGAAAGAAGTAGAAGAGAATGAAGTCAGAAATTCGAATAGTAGTAGATNAATATTAGATAAATTAACAGGGTTT
// * * * - * * -- --- * * * * -* - * * ** * * * -* * - - - |8:A_tuberculatus_Chr01:179827-180032
assembly_reference_sequence TCGCTTTTCATTCATGCGGTAAGAAAATGATAGTGGGACCCACCAATGAGTCAATAACCAATCTACTAGTAGAGATAGAGTAACCTTAGACCAATTAAATTGGTTGCTTTTAATATACAAGCTGCTAGAACCTAGAACACACACCAGATCTTCTACCATTTTCATATAAATAAAAAAATGTCATAAATCTTATCTTTTGCTACGCTTTTCCCACCTTAAATTTCAATACTCTTTTCTCTTAAATCAGTACAACAAGCTTCCACATCAGCTTCAACACAGGCCCGGCCTATGTGCAGGAGCTCCCTAAGCAACAGCTCAGGGCCTCACTTTGTTGGGGGCCCAGTTTTTCAAGGGGCCCTTATTTAAATTTTTGCTCCGGGCCTCGATATTGTCCAAGACGGCTCTGCTTGAACATCGCAAACAATCATAAAACTCTCCAAGGTTTCATCCACACATCACATTGGTCTCCATTTGCTACACATTGGTAAGGTCTAAAATACACATAGGAAGTTTAAACCCTTTATTTCATTTTTGATGATATAGGGATTAGGGAGAGTATTATAATTCTTTCAATAGTGTAATATATGTTGATATATCACACTAATTAATTGTCTATAACATATTTGTTGGTGGTACTATT
SLH_AL_0012 TCGCTTTTCATTCGTGCGGTAAGAAAATGAGAGTGGGACCCACCAATGAGTCAATAACCAATCTACTAGTAGAGATNGAGTAACCTTAGACCAANTAAATTGGTTGCTTTTAATATACRAGCTGCTAGAACCTANAACACACACCAGATCTTCTACCATTTTCATATANATAAAAAAATGTCATAAATCTTANCTTTTGCTACGCTTTTCCCACCTTAAATTTCAATACTCTTTTCTCTTAAATCAGTACAACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
SLH_AL_0014 NCGCTTTTCATTCGTGCGGTAAGAAWATGAGAGTGGGACCCACCAATGAGTCAATAACCAATCTACTAGTAGAGATAGAGTAACCTTAGACCAANTAAATTGGTTGCTTTTAATATACGAGCTNCTAGAACCTANAACACACACCAGATCTTCWACCATTTTCATATANATAAAAAAATGTCATAAATCTTANCTTTTGCTACGYTTTTCCCACCTTAAATTTCAATACTCTTTTCTCTTAAATCASTACAACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCCTATGTGCAGGAGCTCTCTAAGCAGCAGCTCAGGGCCTCACTTTGTTGGGGGCCCAGTTTTTCAAGGGGCCCNTATTTAAACTTTTGCTCCGACCCTCGATATTGTCCAAGACGGCACTGCTTGAACATCGCAAACAATCATAAAACTCTNCAAGNTTTCNTCCACACATCACATTGGTCTCCATTTGCTACACATTGGTAAGGTCNAAAATACACATAGGAAGTTTAAACCCTTTATTTCATATTTGATTATATAGGGATTAGNNNGAGTATTATAATTCTTTCAATAGTGTAATATATGTTGATATNTCACACTAATTAATTGTCTATNAC--ATTTGTTGGTGTTACTATT
SLH_AL_0018 NCGCTTTTCATTCGTGCGGTAAGAAAATGAGAGTGGGACCCACCAATGAGTCAATAACCAATCTACTAGTAGAGATAGAGTAACCTTAGACCAANTAAATTGGTTGCTTTTAATATACAAGCTNCTAGAACCTANAACACACACCAGATCTTCTACCATTTTCATATAA----------------------ANCTTTTGCTACGCTTTTCCCACCTTAAATTTCAATACTCTTTTCTCTTAAATCAGTTCAACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
SLH_AL_0030 TCGCTTTTCATTCGTGCGGTAAGAAAATGAGAGTGGGACCCACCNNNNNNNNNNNNNNNAATCTACTAGTAGAGATWGAGTAACCTTAGACCAANTAAATTGGTTGCTTTTAATATACAAGCTGCTAGAACCTANAACACACACCAGATCTTCTACCATTTTCATATAA----------------------ANCTTTTGCTACGCTTTTCCCACCTTAAATTTCAATACTCTTTTCTCTTAAATCAGTACAACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTTTTCAAGGGGCCCNTATTTAAACTTTTGCTCCGACCCTCGATATTGTCCAAGACGGCTCTGCTTNAACATCGCAAACAATCATAAAACTCTTCAAGATTTCGTCCACACATCACATTGGTCTCCATTTGCTACACATTGGTAAGGTCNAAAATACACATAGGAAGTTTAAACCCTTTATTTCATATTTGATGATATAGGGATTAGNNNGAGTATTATAATTCTTTCAATAGTGTAATATATGTTGATATNTCACACTAATTAATTGTCTATNACATATTTGTTGGTGTTACTATT
SLH_AL_0036 TCGCTTTTCATTCGTGCGGTAAGAAAATGAGAGTGGGACCCACCAATGAGTCAATAACCAATCTACTAGTAGAGATNGAGTAACCTTAGACCAANTAAATTGGTTGCTTTTAATATACRAGCTGCTAGAACCTANAACACACACCAGATCTTCTACCATTTTCATATANATAAAAAAATGTCATAAATCTTANCTTTTGCTACGCTTTTCCCACCTTAAATTTCAATACTCTTTTCTCTTAAATCAGTACAACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
SLH_AL_0042 TCGCTTTTCATTCGTGCGGTAAGAAAATGAGAGTGGGACCCACCNNNNNNNNNNNNNNNAATCTACTAGTAGAGATAGAGTAACCTTAGACCAANTAAATTGGTTGCTTTTAATATACAAGCTGCTAGAACCTANAACACACACCAGATCTTCTACCATTTTCATATANATAAAAAAATGTCATAAATCTTANCTTTTGCTACGCTTTTCCCACCTTAAATTTCAATACTCTTTTCTCTTAAATCASTACAACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTTTTCAAGGGGCCCNTATTTAAACTTTTGCTCCGACCCTCGATATTGTCCAAGACGGCTCTGCTTNAACATCGCAAACAATCATAAAACTCTTCAAGATTTCGTCCACACATCACATTGGTCTCCATTTGCTACACATTGGTAAGGTCNAAAATACACATAGGAAGTTTAAACCCTTTATTTCATATTTGATGATATAGGGATTAGNNNGAGTATTATAATTCTTTCAATAGTGTAATATATGTTGATATNTCACACTAATTAATTGTCTATNACATATTTGTTGGTGTTACTATT
SLH_AL_0048 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGCCTCGATATTGTCCAAGACGGCTCTGCTTG------------AATCATAAAACTCTTCAAGATTTCGTCCACACATCACATTGGTCTCCATTTGCTACACATTGGTAAGGTCGAAAATACACATAGGAAGTTTAAACCCTTTATTTCATATTTGATGATATAGGGATTAGNNNGAGTATTATAATTCTTTCAATAGTGTAATATATGTTGATATNTCACACTAATTAATTGTCTATNACATATTTGTTGGTGTTACTATT
SLH_AL_0064 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGACCAANTAAATTGGTTGCTTTTAATATACAAGCTGCTAGAACCTAGAACACACACCAGATCTTCNACCATTTTCNNATAAATAAAAAAATGTCATAAATCTTATCTTTTGCTACGCTTTTCCCACCATAAATTTCAATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
SLH_AL_0084 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGACCAANTAAATTGGTTGCTTTTAATATACAAGCTGCTAGAACCTAGAACACACACCAGATCTTCNACCATTTTCNNATAAATAAAAAAATGTCATAAATCTTATCTTTTGCTACGCTTTTCCCACCATAAATTTCAATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
SLH_AL_0100 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGACCAANTAAATTGGTTGCTTTTAATATACAAGCTGCTAGAACCTAGAACACACACCAGATCTTCNACCATTTTCNNATAAATAAAAAAATGTCATAAATCTTATCTTTTGCTACGCTTTTCCCACCATAAATTTCAATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
SLH_AL_0101 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGACCAANTAAATTGGTTGCTTTTAATATACAAGCTGCTAGAACCTAGAACACACACCAGATCTTCNACCATTTTCNNATAAATAAAAAAATGTCATAAATCTTATCTTTTGCTACGCTTTTCCCACCATAAATTTCAATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
SLH_AL_0106 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGACCAANTAAATTGGTTGCTTTTAATATACAAGCTGCTAGAACCTAGAACACACACCAGATCTTCNACCATTTTCNNATAAATAAAAAAATGTCATAAATCTTATCTTTTGCTACGCTTTTCCCACCATAAATTTCAATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
// - - - - * - - * * - - - - -* - - - - - - - - |9:A_tuberculatus_Chr01:190356-190995
assembly_reference_sequence CCTGATGAGGAGCAGAAGAATTCAGTGTTCCCTCACCTAGACGATAACTCCCAGGCCAGTAATCAACATAGCAGCTGGAGTTCATATAAGGTAAAACAGGTTGCCCTACAATGATCTGGTGTGATGCAAGACCATGGTTATTAACATAGGCAAAAGCTGGCATCATCGTTAATCCAGCCATGATCATCATTCTTGATTCTTGATTTCTTATATTTGCTTCTCTTCTCTCTTGTTTATGAGCATTTTGATGCCCTCCTA
SLH_AL_0012 CCTGATGAGGAGCAGAAGAATNCAGTGTNCCCTCACNNAGANGATAACTCCCAGGCCANTAATNANNATAGCANCTGGNGTTCATATAAGGTAAAACAGGTTGNCCTACAATGATCTGGTGNGNTGCAAGANCATGGTTATTAACATAGGCAAAAGCTGGCATCATCGTTAATCCAGCCATSATCATCATTYTTGATTCATGATTTCTTATATTTGCTTCTCTTCTCTCTTGTTTATGAGCATTTTGATGCCCTCCTA
SLH_AL_0018 CCTGATGAGGAGCAGAAGAATCCAGTGTTCCCTCACCTAGACGATAACTCCCAGGCCAGTAATTAACATAGCAGCTGGTGTTCATATAAGGTAAAACAGGTTGCCCTACAATGATCTGGTGTGATGCAAGACCATGGTTATTAACATAGGCAAAAGCTGGCATCACNGTTAATCCAGCCATCATCATCATTCTTGATTCATGATTTCTTATATTTGCTTCTCTTCTCTCTTGTTTATGAGCATTTTGATGCCCTCCTA
SLH_AL_0034 CCTGATGAGGAGCAGAAGAATNCAGTGTNCCCTCACNNAGANGATAACTCCCAGGCCANTAATNANNATAGCANCTGGNGTTCATATAAGGTAAAACAGGTTGNCCTACAATGATCTGGTGNGNTGCAAGACCATGGTTATWAACATAGGCAAAAGCTGGCATCATCGTTAAWCCAGCCATCATCATCATTCTTGATTCWTGATTTCTTATATTTGCTTCTCTTCTCTCTTGTTTATGAGCATTTTGATGCCCTCCTA
SLH_AL_0042 CCTGATGAGGAGCAGAAGAATNCAGTGTNCCCTCACNNAGANGATAACTCCCAGGCCANTAATNANNATAGCANCTGGNGTTCATATAAGGTAAAACAGGTTGNCCTACAATGATCTGGTGNGNTGCAAGACCATGGTTATTAACATAGGCAAAAGCTGGCATCATCGTTAATCCAGCCATGATCATCATTCTTGATTCATGATTTCTTATATTTGCTTCTCTTCTCTCTTGTTTATGAGCATTTTGATGCCCTCCTA
SLH_AL_0048 CCTGATGAGGAGCAGAAGAATCCAGTGTTCCCTCACCTAGACGATAACTCCCAGGCCAGTAATCAATATAGCAGCTGGTGTTCATATAAGGTAAAACAGGTTGCCCTACAATGATCTGGTGTGATGCAAGACCATGGTTATTAACATAGGCAAAAGCTGGCATCATCGTTAATCCAGCCATGATCATCATTCTTGATTCTTGATTTCTTATATTTGCTTCTCTTCTCTCTTGTTTATGAGCATTTTGATGCCCTCCTA
// - - - - - - - * - * |10:A_tuberculatus_Chr01:202773-203030
assembly_reference_sequence ACCAAGCTGAGATGAGAGACCAGACATAAAGGCTTCCAGTGCATCTCCAGAATCTTCTTCAACCTTAGGCTCTGATGTCTTGCTCTTCTCTTCCAGAATCAATCTTTTTTTCTCTTCCATTTCATTCAGCAACGCCTCCTTCTTATCCAGTAGAGAATCGGCCGTCTCAACAGATTGTGTATCAGCTGATTTGTTAGCAGGTTTCTGTTTCGT
21040XD-01-08_S40_L002 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGTCTCAACAGATTGTGTATCAGCTGATNNNNNNNNNNNNNNNNNNNNNNN
21040XD-01-09_S41_L002 ACCNAGCTGAGATGAGAGACCAGACATANANGCNTCNAGNGCATCTCCAGNNTCTTNTTCAANCNTAGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTCNTTCTTATCCAGAAGAGAATCGGCNGTCTCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
SLH_AL_0014 ACCGAGCTGAGATGAGAGACCAGACATAAAGGCTTCCAGTGCATCTCCAGAATCTTCTTCAACCTTAGGCTCTGATGTCTTGCTCTTCTCTTCCAGAATCAATCTTTTTTTCTCTTCCATTTCATTCAGCAACGCCTCCTTCTTATCCAGTAGAGAATCGGCCGTCTCAACAGATTGTGTATCAGCTGATTTGTTAGCAGGTTTCTGTTTCGT
SLH_AL_0034 ACCRAGCTGAGATGAGAGACCAGACATAAAGGCTTCCAGTGCATCTCCAGAATCTTCTTCAACCTTAGGCTCTGATGTCTTGCTCTTCTCTTCCAGAATCAATCTTTTTTTCTCTTCCATTTCATTCAGCAACGCCTCCTTCTTATCCAGTAGAGAATCGGCCGTCTCAACAGATTGTGTATCAGCTGATTTGTTAGCAGGTTTCTGTTTCGT
SLH_AL_0036 ACCGAGCTGAGATGAGAGACCAGACATAAAGGCTTCCAGTGCATCTCCAGAATCTTCTTCAACCTTAGGCTCTGATGTCTTGCTCTTCTCTTCCAGAATCAATCTTTTTTTCTCTTCCATTTCATTCAGCAACGCCTCCTTCTTATCCAGTAGAGAATCGGCCGTCTCAACAGATTGTGTATCAGCTGATTTGTTAGCAGGTTTCTGTTTCGT
SLH_AL_0042 ACCGAGCTGAGATGAGAGACCAGACATAAAGGCTTCCAGTGCATCTCCAGAA---TCTTCAACCTTAGGCTCTGATGTCTTGCTCTTCTCTTCCAKAATCAATCTTTTTTTCTCTTCCATTTCATTCAGCAACGCCTCCTTCTTATCCAGTAGAGAATCGGCCGTCTCAACAGATTGTGTATCAGCTGATTTGTTAGCAGGTTTCTGTTTCGT
SLH_AL_0064 ACCGAGCTGAGATGAGAGACCAGACATAAAGGCATCCAGTGCATCTCCAGAATCTTCTTCAACCTTAGGCTCTGATGTCTTGCTCTTCTCTTCCAGAATCAATCTTTTTTTCTCTTCCATTTCATTCAGCAACGCCTCCTTCTTATCCAGAAGAGAATCGGCCGTCTCAACAGATTGTGTATCAGCTGATTTGTTAGCATGTTTCTGTTTCGT
SLH_AL_0100 ACCGAGCTGAGATGAGAGACCAGACATAAAGGCATCCAGTGCATCTCCAGAATCTTCTTCAACCTTAGGCTCTGATGTCTTGCTCTTCTCTTCCAGAATCAATCTTTTTTTCTCTTCCATTTCATTCAGCAACGCCTCCTTCTTATCCAGAAGAGAATCGGCCGTCTCAACAGATTGTGTATCAGCTGATTTGTTAGCATGTTTCTGTTTCGT
SLH_AL_0101 ACCGAGCTGAGATGAGAGACCAGACATAAAGGCATCCAGTGCATCTCCAGAATCTTCTTCAACCTTAGGCTCTGATGTCTTGCTCTTCTCTTCCAGAATCAATCTTTTTTTCTCTTCCATTTCATTCAGCAACGCCTCCTTCTTATCCAGAAGAGAATCGGCCGTCTCAACAGATTGTGTATCAGCTGATTTGTTAGCATGTTTCTGTTTCGT
SLH_AL_0104 ACCGAGCTGAGATGAGAGACCAGACATAAAGGCATCCAGTGCATCTCCAGAATCTTCTTCAACCTTAGGCTCTGATGTCTTGCTCTTCTYTTCCAGAATCAATCTTTTTTTCTCTTCCATTTCATTCAGCAACGCCTCCTTCTTATCCAGAAGAGAATCGGCCGTCTCAACAGATTGTGTATCAGCTGATTTGTTAGCAGGTTTCTGTTTCGT
SLH_AL_0105 ACCGAGCTGAGATGAGAGACCAGACATAAAGGCATCCAGTGCATCTCCAGAATCTTCTTCAACCTTAGGCTCTGATGTCTTGCTCTTCTCTTCCAGAATCAATCTTTTTTTCTCTTCCATTTCATTCAGCAACGCCTCCTTCTTATCCAGAAGAGAATCGGCCGTCTCAACAGATTGTGTATCAGCTGATTTGTTTGCAGGTTTCTGTTTCGT
SLH_AL_0106 ACCGAGCTGAGATGAGAGACCAGACATAAAGGCATCCAGTGCATCTCCAGAATCTTCTTCAACCTTAGGCTCTGATGTCTTGCTCTTCTCTTCCAGAATCAATCTTTTTTTCTCTTCCATTTCATTCAGCAACGCCTCCTTCTTATCCAGAAGAGAATCGGCCGTCTCAACAGATTGTGTATCAGCTGATTTGTTAGCATGTTTCTGTTTCGT
SLH_AL_3066 ACCGAGCTGAGATGAGAGACCAGACATAAAGGCATCCAGTGCATCTCCAGAATCTTCTTCAACCTTAGGCTCTGATGTCTTGCTCTTCTCTTCCAGAATCAATCTTTTTTTCTCTTCCATTTCATTCAGCAACGCCTCCTTCTTATCCAGAAGAGAATCGGCAGTCTCAACAGATTGTGTATCAGCTGATTTGTTTGCAGGTTTCTGTTTCGT
// * * - - * - * * |11:A_tuberculatus_Chr01:211536-211748
assembly_reference_sequence TTTTTTACAATTGCTACGCTTGCATACTAGCCATTATCCATTAAGCTATATTGTCTTACATCTTGTTCTTCATGTATAAAGAAAACAGAGGAAGTACTAATTTGCGAATTGATAACAAGACACACTAATGATGAAAACAC
SLH_AL_0063 TTTTTTACAATTGCTACACTTGCATACTAGCCATTACCCATCAAGCTATATTGTCTAACATCTTATTCTTCATGTATAAAGAAAACAGAGGAAGTACTACTTTGCGAATTGATAACAAGACACACTAATGATGAAAACAG
SLH_AL_0084 TTTTTGACAATTGCTACACTTGCATACTAGCCATTATCCATCAAGCTATATTGTCTTACATCTTATTCTTCATGTATAAAGAAAACAGAGGAAGTACTACTTTGCGAATTGATAACAAGACACACTAATGATGAAAACAT
SLH_AL_0104 TTTTTTACAATTGCTACACTTGCATACCAGCCATTATCCATCAAGCTATATTGTYTTACATTTTATTCTTCAYGTATAAAGAAAACAGAGGAAGTACTACTTTGCGAATTGATAACAAGACACACTAATGATGAAAACAT
SLH_AL_0105 TTTTTTACAATTGCTACACTTGCATACTAGCCATTACCCATCAAGCTATATTGTCTAACATCTTATTCTTCATGTATAAAGAAAACAGAGGAAGTACTACTTTGCGAATTGATAACAAGACACACTAATGATGAAAACAN
SLH_AL_3065 TTTTTTACAATTGCTACACTTGCATACTAGCCATTATCCATCAAGCTATATTGTCTTACATTTTATTCTTCATGTATNNNNNNNNNNNNNNNNNTACTACTTTGCGAATTGATAACAAGACACACTAATGATGAAAACAN
SLH_AL_3066 TTTTTTACAATTGCTACACTTGCATACTTGCCATTACCCATCAAGCTATATTGTCTTACATCTTATTCTTCATGTATNNNNNNNNNNNNNNNNNTACTACTTTGCGAATTGATAACAAGACACACTAATGATGAAAACAG
// - - -- * - - * * - - - *|12:A_tuberculatus_Chr01:216391-216530
assembly_reference_sequence ACATAAGTTCTCCCTGTTTCTTCAAGTATCCCTGCCGCTGCTGATGCATAATTTATCCCTCTCAAGATATGCTTTCCGAACGATGTTATTGAGAAGTATGGTGGTATCAATGGCAATCCCAGATGTCGGGCTTCAATTTTGCACCAAAAAGAAATCAAGTCGGTATCAATATGAGGTTAGCTACATGAACCAAAACAACTGAACGTGATTCAAAAGCTAAAAGCAAAAGTGGGGAATAAATTCCAAGTTACCTCCGTAATCTACAACAGTAAGACCATTGCAAAACCTC
21040XD-01-09_S41_L002 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAGCNNANAGNANNAGNNGGGAATAAATTNCNAGTTACCTCCGTAATCTACAACNGTANNNNNNNNNNNNNNNNNN
SLH_AL_0012 ACATAAGTTCTCCCTGTTTCTTCAAGTATCCCTGCCGCTGCTGATGCATAGTTTATCCCTCTCAAGATATGCTTTCCGAACGATGTTATTGAGAAGTATGGTGGTATCAATGGCAATCCCAGATGTCGGGCTTCAATTTTGCACCAAAAAGAAATCAAGTCGGTATCAATATGAGGTTAGCTACATGAACCAAAACANCTGAACGTGATTCAAAAGCTAAAAGCAAAAGTGGGGAATAAATTCCAAGTTACCTCCGTAATCTACAACAGTAAGACCATTGCAAAACCTC
SLH_AL_0014 ACATAAGTTCTCCCTGTTTCTTCAAGTATCCCTGCCGCTGCTGATGCATAGTTTATCCCTCTCAAGATATGCTTTCCGAACGATGTTATTGAGAAGTATGGTGGTATCAAYGGCAATCCCAGATGTCGGGCTTCAATTTTGCACCAAAAAGAAATCAAGTCGGYATCAATATGAGGTTAGCTACATGAACCAAAACANCTGAACGTGATTCAAAAGCTAAAAGCAAAAGTGGGGAATAAATTYCAAGTTACCTCCGTAATCTACAACAGTAAGACCATTGCAAAACCTC
SLH_AL_0018 ACATAAGTTCTCCCTGTTTCTTCAAGTATCCCTGCCGCTGCTGATGCATAGTTTATCCCTCTCAAGATATGCTTTCCGAACGATGTTATTGAGAAGTATGGTGGTATCAAYGGCAATCCCAGATGTCGGGCTTCAATTTTGCACCAAAAAGAAATCAAGTCGGYATCAATATGAGGTTAGCTASATGAACCAAAACANCTGAACGTGATTCAAAAGCTAAAAGCAAAAGTGGGGAATAAATTYCAAGTTACCTCCGTAATCTACAACAGTAAGACCATTGCAAAACCTC
SLH_AL_0030 ACATAAGTTCTCCCTGTTTCTTCAAGTATCCCTGCCGCTGCTGATGCATAATTTATCCCTCTCAAGATATGCTTTCCGAACGATGTTATTGAGAAGTATGGTGGTATCAATGGCAATCCCAGATGTCGGGCTTCAATTTTGCACCAAAAAGAAATCAAGTCAGCATCAATATGAGGTTAGCTACATGAACCAAAACANCTGAACGTGATTCAAAAGCTAAAAGCAAAAGTGGGGAATAAATTTCAAGTTACCTCCGTAATCTACAACAGTAAGACCATTGCAAAACCTC
SLH_AL_0034 ACATAAGTTCTCCCTGTTTCTTCAAGTATCCCTGCCGCTGCTGATGCATAGTTTATCCCTCTCAAGATATGCTTTCCGAACGATGTTATTGAGAAGTATGGTGGTATCAAYGGCAATCCCAGATGTCGGGCTTCAATTTTGCACCAAAAAGAAATCAAGTCRGCATCAATATGAGGTTAGCTACATGAACCAAAACANCTGAACGTGATTCAAAAGCTAAAAGCAAAAGYGGGGAATAAATTTCAAGTTACCTCCGTAATCTACAACAGTAAGACCATTGCAAAACCTC
SLH_AL_0036 ACATAAGTTCTCCCTGTTTCTTCAAGTATCCCTGCCGCTGCTGATGCATAATTTATCCCTCTCAAGATATGCTTCCCGAACGATGTTATTGAGAAGTATGGTGGTATCAACGGCAATCCGAGATGTCGGGCTTCAATTTTGCACCAAAAAGAAATCAAGTCGGTATCAATACGAGGTTAGCTANNTGAACCAAAACANCTGAACGTNATTCAAAAGCTAAAAGCATGAGTCGGGAATAAATTTCAAGTTACCTCCGTAATCTACAACAGTAAGACCATTGCAAAACCTC
SLH_AL_0042 ACATAAGTTCTCCCTGTTTCTTCAAGTATCCCTGCCGCTGCTGATGCATAGTTTATCCCTCTCAAGATATGCTTTCCGAACGATGTTATTGAGAAGTATGGTGGTATCAACGGCAATCCCAGATGTCGGGCTTCAATTTTGCACCAAAAAGAAATCAAGTCGGCATCAATATGAGGTTAGCTACATGAACCAAAACANCTGAACGTGATTCAAAAGCWWAAAGMAAAAGTGGGGAATAAATTTCAAGTTACCTCCGTAATCTACAACAGTAAGACCATTGCAAAACCTC
SLH_AL_0048 ACATAAGTTCTCCCTGTTTCTTCAAGTATCCCTGCCGCTGCTGATGCATAGTTTATCCCTCTCAAGATATGCTTTCCGAACGATGTTATTGAGAAGTATGGTGGTATCAAYGGCAATCCCAGATGTCGGGCTTCAATTTTGCACCAAAAAGAAATCAAKTCGGCATCAATATGAGGTTAGCTACATGAACCAAAACANCTGAACGTGATTCAAAAGCTAAAAGCAAAAGTGGGGAATAAATTTCAAGTTACCTCCGTAATCTACAACAGTAAGACCATTGCAAAACCTC
SLH_AL_0064 ACGTAAGTTCTCCCTGTTTCTTCAAGTATTCCTGCCGCTGCTGATGCATAATTTATGCCTCTCAATATATGCTTTCCGAACGATGTTATTGAGAAGTATGGTGGTATCAACGGCAATCCAAGATGTCGTGCTTCAATTTTGCACCAAAAAGAAATCGAGTCGGTATCAATATGAGGTTAGCTACATGAACCAAAACANCTGAACGTGATTCATAAGCTAAAAGCAAAAGTGGGGAATAAATTACAAGTTACCTCCGTAATCTACAACCGTAAGACCATTGCAAAACCTC
SLH_AL_0100 ACGTAAGTTCTCCCTGTTTCTTCAAGTATTCCTGCCGCTGCTGATGCATAATTTATGCCTCTCAATATATGCTTTCCGAACGATGTTATTGAGAAGTATGGTGGTATCAACGGCAATCCAAGATGTCGTGCTTCAATTTTGCACCAAAAAGAAATCGAGTCGGTATCAATATGAGGTTAGCTACATGAACCAAAACANCTGAACGTGATTCATAAGCTAAAAGCAAAAGTGGGGAATAAATTACAAGTTACCTCCGTAATCTACAACCGTAAGACCATTGCAAAACCTC
SLH_AL_0101 ACGTAAGTTCTCCCTGTTTCTTCAAGTATTCCTGCCGCTGCTGATGCATAATTTATGCCTCTCAATATATGCTTTCCGAACGATGTTATTGAGAAGTATGGTGGTATCAACGGCAATCCAAGATGTCGTGCTTCAATTTTGCACCAAAAAGAAATCGAGTCGGTATCAATATGAGGTTAGCTACATGAACCAAAACANCTGAACGTGATTCATAAGCTAAAAGCAAAAGTGGGGAATAAATTACAAGTTACCTCCGTAATCTACAACCGTAAGACCATTGCAAAACCTC
SLH_AL_0104 ACGTAAGTTCTCCCTGTTTCTTCAAGTATTCCTGCCGCTGCTGATGCATAATTTATTCCTCTCAAGATATGCTTTCCGAACGATGTTATTGAGAAGTATGGTGGTATCAACGGCAATCCGAGATGTCGTGCTTCAATTTTGCACCAAAAAGAAATCGAGTCGGTATCAATATGAGGTTAGCTACATGAACCAAAACANCTGAACATGATTCATAAGCTAAAAGCAAAAGTGGGGAATAAATTACAAGTTACCTCCGTAATCTACAACCGTAAGACCATTGCAAAACCTC
SLH_AL_0105 ACGTAAGTTCTCCCTGTTTCTTCAAGTATTCCTGCCGCTGCTGATGCATAATTTATGCCTCTCAATATATGCTTTCCGAACGATGTTATTGAGAAGTATGGTGGTATCAACGGCAATCCGAGATGTCGTGCTTCAATTTTGCACCAAAAAGAAATCGAGTCGGTATCAATATGAGGTTAGCTACATGAACCAAAACANCTGAACGTGATTCATAAGCTAACAGCAAAAGTGGGGAATAAATTACAAGTTACCTCCGTAATCTACAACCGTAAGACCATTGCAAAACCTC
SLH_AL_0106 ACGTAAGTTCTCCCTGTTTCTTCAAGTATTCCTGCCGCTGCTGATGCATAATTTATGCCTCTCAATATATGCTTTCCGAACGATGTTATTGAGAAGTATGGTGGTATCAACGGCAATCCAAGATGTCGTGCTTCAATTTTGCACCAAAAAGAAATCGAGTCGGTATCAATATGAGGTTAGCTACATGAACCAAAACANCTGAACGTGATTCATAAGCTAAAAGCAAAAGTGGGGAATAAATTACAAGTTACCTCCGTAATCTACAACCGTAAGACCATTGCAAAACCTC
SLH_AL_3065 ACGTAAGTTCTCCCTGTTTCTTCAAGTATTCCTGCCGCTGCTGATGCATAATTTATTCCTCTCAAGATATGCTTTCCGAACGATGTTATTGAGAAATATGGTGGTATCAACGGCAATCCGAGATGTCGTGCTTCAATTTTGCACCAAAAAGAAATCGAGTCGGTATCAATATGAGGTTAGCTACATGAACCAAAACANCTGAACATGATTCATAAGCTAAAAGCAAAAGTGGGGAATAAATTACAAGTTACCTCCGTAATCTACAACCGTAAGACCATTGCAAAACCTC
// * * * * * - - * * * * - * * - - * * -- - - -- -- * * |13:A_tuberculatus_Chr01:274089-274377
assembly_reference_sequence TTAAGCTGATGGTTAAAGCCCTAGGACATGTTATATAATCTATCATTTCTCGGACCAACTAGTAACCAAAGTAGTAGTTAATATCGATAGTAAAGTTAGATGGACATAAATCTATGTTGTCTGATTTCGTAGTGTCATTGACAGCAGACTAGAAGCTGTCTCGCCATTGGCGAGCTTGATCTGATAAATCGAAATGAGTACACCTGGTTCTAAAACCCATTAATATGTGTAATCTTAATAGATCGAATTTCATTTCGTGCATCTTCTCTTATTTGGATTATTGTTCTGTACTGATGGAAGTGTTTAAGGATGTTAGTTGCAAAAATGTATTTAAACCTTGAAGTTATTCATATATGGCATATGCATATTAAACCTATATGC
SLH_AL_0012 TTAAGCTGATGGTTAAARCTCTAGGACATGTTATATAATCTATCGTTTCTCGGAGCAGCTATTAACCAAAGTAGTAGTTRATATCGATAGAAAAGTTAGATTGACATAAATCTATGTTGTCTGATTTCGTAGTGTCATTGACAGCAGANTAGAAGCTGTCTCGCCANTGGCGANCTTGATCNGATAAATCNAAATGAGTANACCTGGTTNTAAAACCCANNAATATGTGTAATCTTAATAGATNGAATTTCATTTCGTGCATCTT---TTATTTGGATTATTGTTCTGTACTGATGGAAGTGTTTAAGGATGTTAGTTGCAAAAATGTATTTAAACCTTGAAGTTATTCATATATGGCATATGCATATTAAACYTATATGC
SLH_AL_0014 TTAAGCTGATGGTTAAAGCTCTAGGACATGTTATATAATCTATCGTTTCTCGGAGCAGCTATTAACCAAAGTAGTAGTTAATATCGATAGAAAAGTTAGATTGACANAAATCTATGNTGNCNGNTTTCGNAGTGTCATTGACAGCAGANTAGAAGCTGTCTCGCCANTGGCGANCTTGATCNGATAAATCNAAATGAGTANACCTGGTTNTAAAACCCANNAATATGTGTAATCTTAATAGATNGAATTTCATTTCGTGCATCTT---TTATTTGGATTATTGTTCTGTACTGATGGAAGTGTTTAAGGATGTTAGTTGCAAAAATGTATTTAAACCTTGAAGTTATTCATATATGGCATATGCATATTAAACCTATATGC
SLH_AL_0018 TTAAGCTGATGGTCAAAGCCTTAGGACATGTTATATAATTTATCATTTCTCGGACCAACTAGTAACCAAAGTAGTAGTTAATATCGATAGTAAAGTTAGATGGACATAAATCTATGTTGTCTGATTTCGT--TGTCATTGACAGCAGANTAGAAGCTGTCTCGCCANTGGCGANCTTGATCNGATAAATCNAAATGAGTANACCTGGTTNTAAAACCCANNAATATGTGTAATCTTAATAGATNGAATTTCATTTCGTGCATCTTCTCTTATTTGGATTATTGTTCTGTACTGATGGAAGTGTTTAAGGATGATAGTTGCAAAAATGTATTTAAACCTTGAAGTTATTCATATATGGCATATGCATAATAATCCTATATGC
SLH_AL_0036 TTAAGCTGATGGTYAAAGCCYTAGGACATGTTATATAATYTATCATTTCTCGGAYCAACTAGTAACCAAAGTAGTAGTTAATATCGATAGTAAAGTTAGATGGACATAAATCTATGTTGTCWGATTTCGT--TGTCATTGACAGCAGANTAGAAGCTGTCTCGCCANTGGCGANCTTGATCNGATAAATCNAAATGAGTANACCTGGTTNTAAAACCCANNAATATGTGTAATCTTAATAGATNGAATTTCATTTCGTGCATCTT---TTATTTGGATTATTGTTCTGTACTGATGGAAGTGTTTAAGGATGWTAGTTGCAAAAATGTATTTAAACCTTGAAGTTATTCATATATGGCATATGCATAWTAAWCCTATATGC
SLH_AL_0100 TTAAGTAGATGGTTAAAGCCCTAGGACATGTTATATAATCTATCATTTCTNGNACCAACTTGTNACCAAAGTAGTAGTTAATATCGATCGTAAAGTTAGATGGACATAAATGTATGTTGTCTGATTTCGTAGTGTCATTGACAGCAGANTAGAAGCTGTCTCGCCANTGGCGANCTTGATCNGATAAATCNAAATGAGTANACCTGGTTNTAAAACCCANNAATATGTGTAATCTTAATAGATCGAATTTCATTTCGTGCATCTTCTCTTGTTTGGATTATTGTTCTGTACTAATGGAAGTCTTTAAGGATGTTAGCTGCAAAAATGTATTTAAACCTTGAAGTTATTCATGTACGGCATATGCATATTAAACCTATATGC
SLH_AL_0101 TTAAGTAGATGGTTAAAGCCCTAGGACATGTTATATAATCTATCATTTCTNGNACCAACTTGTNACCAAAGTAGTAGTTAATATCGATCGTAAAGTTAGATGGACATAAATGTATGTTGTCTGATTTCGTAGTGTCATTGACAGCAGANTAGAAGCTGTCTCGCCANTGGCGANCTTGATCNGATAAATCNAAATGAGTANACCTGGTTNTAAAACCCANNAATATGTGTAATCTTAATAGATCGAATTTCATTTCGTGCATCTTCTCTTGTTTGGATTATTGTTCTGTACTAATGGAAGTCTTTAAGGATGTTAGCTGCAAAAATGTATTTAAACCTTGAAGTTATTCATGTACGGCATATGCATATTAAACCTATATGC
SLH_AL_0105 TTAAGTAGATGGTTAAAGCCCTAGGACATGTTATATGATCTATCATTTCTNGCACCAACTTGTNACCAAAGTAGTAGTTGATATCGATAGTAAAGTTAGATGGACATAAATGTATGTTGTCTGNTTTCGNAGTGTCATTGACAGCAGANTAGAAGCTGTCTCGCCANTGGCGANCTTGATCNGATAAATCNAAATGAGTANACCTGGTTNTAAAACCCANNAATATGTGTAATCTTAATAGATNGAATTTCATTTCGTGCATCTTCTCTTATTTGGATTATTGTTCTGTACTAATGGAAGTCTTTAAGGATGTTAGTTGCAAAAATGTATTTAAACCTTGAAGTTATTCATGTACGGCATATGCATATTAAACCTATATGC
SLH_AL_0106 TTAAGTAGATGGTTAAAGCCCTAGGACATGTTATATAATCTATCATTTCTNGNACCAACTTGTNACCAAAGTAGTAGTTAATATCGATCGTAAAGTTAGATGGACATAAATGTATGTTGTCTGATTTCGTAGTGTCATTGACAGCAGANTAGAAGCTGTCTCGCCANTGGCGANCTTGATCNGATAAATCNAAATGAGTANACCTGGTTNTAAAACCCANNAATATGTGTAATCTTAATAGATCGAATTTCATTTCGTGCATCTTCTCTTGTTTGGATTATTGTTCTGTACTAATGGAAGTCTTTAAGGATGTTAGCTGCAAAAATGTATTTAAACCTTGAAGTTATTCATGTACGGCATATGCATATTAAACCTATATGC
SLH_AL_3066 TTAAGTAGATGGTTAAAGCCCTAGGACATGTTATATGATCTATCATTTCTNGCACCAACTTGTNACCAAAGTAGTAGTTGATATCGATAGTAAAGTTAGATGGACATAAATGTATGTTGTCTGNTTTCGNAGTGTCATTGACAGCAGANTAGAAGCTGTCTCGCCANTGGCGANCTTGATCNGATAAATCNAAATGAGTANACCTGGTTNTAAAACCCANNAATATGTGTAATCTTAATAGATCGAATTTCATTTCGTGCATCTTCTCTTATTTGGATTATTGTTCTGTACTAATGGAAGTCTTTAAGGATGTTAGTTGCAAAAATGTATTTAAACCTTGAAGTTATTCATGTACGGCATATGCATATTAAACCTATATGC
// ** * - ** * * * * * * ** * * * * * - * * * * * * * * * - |14:A_tuberculatus_Chr01:276432-276812
assembly_reference_sequence TTAATTGAATATAGTATTAAAAAGTCAACATGATGGGAGGTTTCACTACAAGATTGAATCTCATCGACCTCTCATTTCAATTGAAGTTTATAACGCCAAATTGATGAGAGTCTATGTATATCCACAATTCTAGGCCAAACTGTTTTCATATGAAGAGGTTATTTAATTATATAACATATCTCATAACCTCAATTATCAACTTATTGACTTTATTTTTAGTTATCACTATATATTGGCTTTAAATTTCTTATTTTTCTTCCCATTCCATTGTTGAATAACTATTTCCACAAATCTAAAAAAATAAAATTTTAAAAGGGAAAATATTGAAAAAATGGATTCATTTAGGTTGA
SLH_AL_0012 TTAATTGAATATAGTATTAAAAAGTCAACATGACGGGAGGTTTC---ACAAGATTAAATCTCATCGACCTCTCATTTCAATTGAAGTTTATAACGCCAAATTGATGAGAGTCTATGTATATCCACAATTCTAGGCCAAACTGTTTTCANATGAAGAGGTTATTTAATTATATAACATANCTCATAACNTCAATNATNAACTTATTGACTTTATTTTTAGTTATCACTATATATTGGCTTTAAATTTCTTATTTTTCTTCCCATTCCATTGTTGAATAACTATTTCCACAAATCTAAAAAAATAAAATTTTAAAAGGGGAAATATTGAAAAAATGGATTCATTTAGGTTGA
SLH_AL_0018 TTAATTGAATATAGTATTAAAAAGTCAACATGACGGGAGGTTTCACTACAAGATTGAATCTCATCGACCTCTCATTTCAATTGAAGTTTATAACGCCAAATTGATGAGAGTCTATGTATATCCACAATTCTAGGCCAAANTGTTTTCANATGAAGAGGTTATTTAATTATATAACATANCTCATAACNTCAATNATNAACTTATTGACTTTATTTTTAGTTATCACTATATATTGGCTTTAAATTTCTTATTTTTCTTCCCATTCCATTGTTGAATAACTATTTCCACAAATCTAAAAAAATAAAATTTTAAAAGGGRAAATATTGAAAAAATGGATTCATTTAGGTTGA
SLH_AL_0034 TTAATTGAATATAGTATTAAAAAGTCAACATGACGGKAGGTTTCACTACAAGATTGAATCTCATCGACCTCTCATTTCAATTGAAGTTTATAACGCCAAATTGATGAGAGTCTATGTATATCCACAATTCTAGGCCAAANTGTTTTCANATGAAGAGGTTATTTAATTATATAACATANCTCATAACNTCAATNATNAACTTATTGACTTTATTTTTAGTTATCACTATATATTGGCTTTAAATTTCTTATTTTTCTTCCCATTCCATTGTTGGATAACTATTTCCACAAATYTAAAAAAATAAAATTTTAAAAGGGGAAATATTGAAAAAATGGATTCATTTAGGTTGA
SLH_AL_0036 TTAATTGAATATAGTATTAAAAAGTCAACATGACGGGAGGTTTCACTACAAGATTGAATCTCATCGACCTCTCATTTCAATTGAAGTTTATAACGCCAAATTGATGAGAGTCTATGTATATCCACAATTCTAGGCCAAANTGTTTTCANATGAAGAGGTTATTTAATTATATAACATANCTCATAACNTCAATNATNAACTTATTGACTTTATTTTTAGTTATCACTATATATTGGCTTTAAATTTCTTATTTTTCTTCCCATTCCATTGTAGAATAACTATTTCCACAAATCTAAAAAAATAAAATTTTAAAAGGGAAAATATTGAAAAAATGGATTCATTTAGGTTGA
SLH_AL_0042 TTAATTGAATATAGTATTAAAAAGTCAACATGATGGGAGGTTTCACTACAAGATTGAATCTCATCGACCTCTCATTTCAATTGAAGTTTATAACGCCAAATTGATGAGAGTCTATGTATATCCACAATTCTAGGCCAAANTGTTTTCANATGAAGAGGTTATTTAATTATATAACATANCTCATAACNTCAATNATNAACTTATTGACTTTATTTTTAGTTATCACTATATATTGGCTTTAAATTTCTTATTTTTCTTCCCATTCCATTGTTGAATAACTATTTCCACAAATCTAAAAAAATAAAATTTTAAAAGGGAAAATATTGAAAAAATGGATTCATTTAGGTTGA
// * - - - - - * |15:A_tuberculatus_Chr01:280635-280984