Releases

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Release summary
  • Strains: 913
  • WGS strains: 773
  • Isotypes: 403
  • Genome WS276

Release Notes

The 20200815 release includes genotypes from whole-genome sequences and reduced representation (RAD) sequencing. Genotypes are compared for concordance, and strains that are 99.95% identical to each other are grouped into isotypes. One strain within each isotype is the reference strain for that isotype. To look up isotype assignment, see Alignment Data tab. All isotype reference strains are available on CeNDR.

Datasets


Dataset Description Download
Strain Data Includes strain, isotype, location information, and more. CelegansStrainData.tsv
Soft-Filtered Variants The soft-filtered VCF includes all variants and annotations called by the GATK pipeline. The QC status of each variant (INFO field=FILTER) and genotype (Format Field=FT) is specified by a VCF Field. All Strains
WI.20200815.soft-filter.vcf.gz
WI.20200815.soft-filter.vcf.gz.csi

Isotypes
WI.20200815.soft-filter.isotype.vcf.gz
WI.20200815.soft-filter.isotype.vcf.gz.csi
Hard-Filtered Variants The hard-filtered VCF includes only high-quality variants after all variants and genotypes with a failed QC status are removed. To obtain vcf for a single or a subset of strains, use bcftools view --samples All Strains
WI.20200815.hard-filter.vcf.gz
WI.20200815.hard-filter.vcf.gz.csi

Isotypes
WI.20200815.hard-filter.isotype.vcf.gz
WI.20200815.hard-filter.isotype.vcf.gz.csi
Imputed Variants The imputed VCF includes all the variants from the hard-filtered Isotype VCF, but all missing genotypes have been imputed using Beagle v5.1. Isotypes
WI.20200815.impute.isotype.vcf.gz
WI.20200815.impute.isotype.vcf.gz.csi
Reference Genome FASTA (WS276) The reference genome build from Wormbase used for alignment and annotation. c_elegans.PRJNA13758.WS276.genomic.fa.gz
Transposon Calls We have performed transposon calling for a subset of isotypes as part of Laricchia et al. tes_cender.bed
Tree Tree generated using neighbour-joining algorithm as implemented in QuickTree in Newick and PDF format. All Strains
WI.20200815.hard-filter.min4.tree (PDF)

Isotype
WI.20200815.hard-filter.isotype.min4.tree (PDF)
Haplotypes Haplotypes for isotypes were calculated and plotted as described in Lee et al. haplotype.png
haplotype.pdf
Sweep Haplotypes The most frequent haplotype that covers at least 25% of the chromosome and is found on chromosome centers was determined and classified as a selective sweep. For more details, see Andersen et al. and Lee et al.. The plot shows red (swept), gray (non-swept), and white (not classified) regions. sweep.pdf
sweep_summary.tsv
Hyper-Divergent Regions The hyper-divergent regions are characterized by higher-than-average density of small variants and large genomic spans where short sequence reads fail to align to the N2 reference genome. They were identified as described in Lee et al. divergent_regions_strain.bed.gz
Download BAMs Script You can batch download individual strain BAMs using this script. download_bams.sh

Alignment (BAM)

Only strains with whole-genome sequencing data have BAM files for download. If you do not see a strain, check the Strain Issues tab. Some strains have been flagged and removed from distribution and analysis pipelines for a variety of reasons.

Strain Isotype Strain BAM
AB1 AB1 BAM / bai
BRC20067 BRC20067 BAM / bai
    BRC20113 BRC20067 BAM / bai
BRC20263 BRC20263 BAM / bai
ECA243 CB4851 BAM / bai
    DR1344 CB4851
    RW7000 CB4851
CB4852 CB4852 BAM / bai
    JU1563 CB4852
ECA246 CB4853 BAM / bai
    CB3198 CB4853
    DR1350 CB4853
    ECA245 CB4853 BAM / bai
CB4854 CB4854 BAM / bai
    CB3196 CB4854
    CB3197 CB4854
ECA248 CB4855 BAM / bai
CB4856 CB4856 BAM / bai
    ECA260 CB4856
ECA250 CB4857 BAM / bai
    CB3199 CB4857
    DR1345 CB4857
    ECA249 CB4857 BAM / bai
ECA251 CB4858 BAM / bai
    AB2 CB4858
    AB3 CB4858
    AB4 CB4858 BAM / bai
    CX11258 CB4858
    CX11278 CB4858
    CX11305 CB4858
    CX11317 CB4858
    ECA247 CB4858
    JU1960 CB4858 BAM / bai
CB4932 CB4932 BAM / bai
CX11254 CX11254 BAM / bai
CX11262 CX11262 BAM / bai
    CX11294 CX11262
CX11264 CX11264 BAM / bai
CX11271 CX11271 BAM / bai
    CX11319 CX11271
CX11276 CX11276 BAM / bai
    CX11316 CX11276
CX11285 CX11285 BAM / bai
    CX11321 CX11285
CX11292 CX11292 BAM / bai
    CX11259 CX11292
CX11307 CX11307 BAM / bai
CX11314 CX11314 BAM / bai
CX11315 CX11315 BAM / bai
    CX11268 CX11315
DL200 DL200 BAM / bai
DL226 DL226 BAM / bai
DL238 DL238 BAM / bai
ECA1069 ECA1069 BAM / bai
ECA1074 ECA1074 BAM / bai
    ECA1070 ECA1074 BAM / bai
    ECA1071 ECA1074 BAM / bai
    ECA1072 ECA1074 BAM / bai
    ECA1073 ECA1074 BAM / bai
ECA1185 ECA1185 BAM / bai
ECA1186 ECA1186 BAM / bai
ECA1191 ECA1191 BAM / bai
ECA1193 ECA1193 BAM / bai
ECA1194 ECA1194 BAM / bai
ECA1195 ECA1195 BAM / bai
ECA1208 ECA1208 BAM / bai
    ECA1203 ECA1208 BAM / bai
    ECA1205 ECA1208 BAM / bai
ECA1216 ECA1216 BAM / bai
    ECA1215 ECA1216 BAM / bai
    ECA1217 ECA1216 BAM / bai
    ECA1218 ECA1216 BAM / bai
ECA1223 ECA1223 BAM / bai
    ECA1224 ECA1223 BAM / bai
ECA1225 ECA1225 BAM / bai
    ECA1222 ECA1225 BAM / bai
    ECA1226 ECA1225 BAM / bai
ECA1228 ECA1228 BAM / bai
ECA1229 ECA1229 BAM / bai
    ECA1233 ECA1229 BAM / bai
    ECA1241 ECA1229 BAM / bai
ECA1232 ECA1232 BAM / bai
ECA1237 ECA1237 BAM / bai
    ECA1234 ECA1237 BAM / bai
    ECA1236 ECA1237 BAM / bai
ECA1238 ECA1238 BAM / bai
    ECA1239 ECA1238 BAM / bai
ECA1240 ECA1240 BAM / bai
ECA1242 ECA1242 BAM / bai
ECA1247 ECA1247 BAM / bai
    ECA1246 ECA1247 BAM / bai
    ECA1272 ECA1247 BAM / bai
    ECA1274 ECA1247 BAM / bai
ECA1251 ECA1251 BAM / bai
    ECA1250 ECA1251 BAM / bai
ECA1253 ECA1253 BAM / bai
ECA1255 ECA1255 BAM / bai
    ECA1256 ECA1255 BAM / bai
ECA1257 ECA1257 BAM / bai
    ECA1258 ECA1257 BAM / bai
ECA1260 ECA1260 BAM / bai
    ECA1259 ECA1260 BAM / bai
ECA1261 ECA1261 BAM / bai
ECA1269 ECA1269 BAM / bai
    ECA1267 ECA1269 BAM / bai
    ECA1268 ECA1269 BAM / bai
ECA1271 ECA1271 BAM / bai
    ECA1270 ECA1271 BAM / bai
ECA1276 ECA1276 BAM / bai
    ECA1277 ECA1276 BAM / bai
ECA1278 ECA1278 BAM / bai
ECA1281 ECA1281 BAM / bai
    ECA1262 ECA1281 BAM / bai
    ECA1263 ECA1281 BAM / bai
    ECA1264 ECA1281 BAM / bai
    ECA1273 ECA1281 BAM / bai
    ECA1275 ECA1281 BAM / bai
    ECA1279 ECA1281 BAM / bai
    ECA1282 ECA1281 BAM / bai
ECA1283 ECA1283 BAM / bai
ECA1284 ECA1284 BAM / bai
    ECA1285 ECA1284 BAM / bai
ECA1286 ECA1286 BAM / bai
    ECA1290 ECA1286 BAM / bai
ECA1287 ECA1287 BAM / bai
ECA1288 ECA1288 BAM / bai
    ECA1265 ECA1288 BAM / bai
    ECA1266 ECA1288 BAM / bai
ECA1289 ECA1289 BAM / bai
ECA1293 ECA1293 BAM / bai
    ECA1294 ECA1293 BAM / bai
ECA1298 ECA1298 BAM / bai
    ECA1292 ECA1298 BAM / bai
    ECA1295 ECA1298 BAM / bai
    ECA1296 ECA1298 BAM / bai
ECA1413 ECA1413 BAM / bai
    ECA1389 ECA1413 BAM / bai
    ECA1391 ECA1413 BAM / bai
    ECA1415 ECA1413 BAM / bai
ECA1465 ECA1465 BAM / bai
ECA1467 ECA1467 BAM / bai
ECA1493 ECA1493 BAM / bai
ECA1515 ECA1515 BAM / bai
ECA189 ECA189 BAM / bai
    ECA190 ECA189 BAM / bai
    ECA192 ECA189 BAM / bai
    ECA193 ECA189 BAM / bai
    ECA393 ECA189 BAM / bai
    ECA395 ECA189 BAM / bai
    ECA394 ECA189 BAM / bai
ECA191 ECA191 BAM / bai
ECA2677 ECA2677 BAM / bai
    ECA1201 ECA2677 BAM / bai
ECA2678 ECA2678 BAM / bai
ECA2679 ECA2679 BAM / bai
    ECA1212 ECA2679 BAM / bai
ECA2686 ECA2686 BAM / bai
    ECA1243 ECA2686 BAM / bai
ECA347 ECA347 BAM / bai
ECA348 ECA348 BAM / bai
ECA349 ECA349 BAM / bai
    ECA350 ECA349 BAM / bai
ECA36 ECA36 BAM / bai
ECA363 ECA363 BAM / bai
ECA369 ECA369 BAM / bai
ECA372 ECA372 BAM / bai
ECA396 ECA396 BAM / bai
    ECA397 ECA396 BAM / bai
    ECA398 ECA396 BAM / bai
    ECA399 ECA396 BAM / bai
ECA592 ECA592 BAM / bai
ECA593 ECA593 BAM / bai
ECA594 ECA594 BAM / bai
ECA640 ECA640 BAM / bai
ECA701 ECA701 BAM / bai
    ECA702 ECA701 BAM / bai
ECA703 ECA703 BAM / bai
ECA705 ECA705 BAM / bai
    ECA822 ECA705 BAM / bai
ECA706 ECA706 BAM / bai
ECA710 ECA710 BAM / bai
ECA712 ECA712 BAM / bai
    ECA711 ECA712 BAM / bai
    ECA713 ECA712 BAM / bai
    ECA714 ECA712 BAM / bai
    ECA715 ECA712 BAM / bai
ECA722 ECA722 BAM / bai
ECA723 ECA723 BAM / bai
    ECA728 ECA723 BAM / bai
    ECA729 ECA723 BAM / bai
ECA724 ECA724 BAM / bai
    ECA725 ECA724 BAM / bai
    ECA726 ECA724 BAM / bai
    ECA727 ECA724 BAM / bai
    ECA1441 ECA724 BAM / bai
ECA730 ECA730 BAM / bai
ECA732 ECA732 BAM / bai
ECA733 ECA733 BAM / bai
    ECA731 ECA733 BAM / bai
ECA738 ECA738 BAM / bai
    ECA734 ECA738 BAM / bai
    ECA735 ECA738 BAM / bai
    ECA736 ECA738 BAM / bai
    ECA737 ECA738 BAM / bai
ECA740 ECA740 BAM / bai
ECA741 ECA741 BAM / bai
ECA742 ECA742 BAM / bai
ECA743 ECA743 BAM / bai
ECA744 ECA744 BAM / bai
    ECA1213 ECA744 BAM / bai
    ECA1214 ECA744 BAM / bai
ECA745 ECA745 BAM / bai
    ECA747 ECA745 BAM / bai
ECA746 ECA746 BAM / bai
ECA760 ECA760 BAM / bai
    ECA739 ECA760 BAM / bai
    ECA749 ECA760 BAM / bai
    ECA752 ECA760 BAM / bai
    ECA753 ECA760 BAM / bai
    ECA754 ECA760 BAM / bai
    ECA758 ECA760 BAM / bai
    ECA769 ECA760 BAM / bai
    ECA779 ECA760 BAM / bai
    ECA780 ECA760 BAM / bai
    ECA784 ECA760 BAM / bai
    ECA785 ECA760 BAM / bai
    ECA808 ECA760 BAM / bai
    ECA1244 ECA760 BAM / bai
    ECA1245 ECA760 BAM / bai
    ECA1291 ECA760 BAM / bai
    ECA1385 ECA760 BAM / bai
ECA768 ECA768 BAM / bai
    ECA772 ECA768 BAM / bai
ECA777 ECA777 BAM / bai
ECA778 ECA778 BAM / bai
    ECA707 ECA778 BAM / bai
    ECA708 ECA778 BAM / bai
    ECA709 ECA778 BAM / bai
    ECA721 ECA778 BAM / bai
    ECA756 ECA778 BAM / bai
    ECA757 ECA778 BAM / bai
    ECA763 ECA778 BAM / bai
    ECA764 ECA778 BAM / bai
    ECA765 ECA778 BAM / bai
    ECA766 ECA778 BAM / bai
    ECA767 ECA778 BAM / bai
    ECA781 ECA778 BAM / bai
    ECA810 ECA778 BAM / bai
    ECA811 ECA778 BAM / bai
ECA807 ECA807 BAM / bai
    ECA716 ECA807 BAM / bai
    ECA717 ECA807 BAM / bai
    ECA718 ECA807 BAM / bai
    ECA720 ECA807 BAM / bai
    ECA770 ECA807 BAM / bai
ECA812 ECA812 BAM / bai
    ECA704 ECA812 BAM / bai
    ECA719 ECA812 BAM / bai
    ECA748 ECA812 BAM / bai
    ECA750 ECA812 BAM / bai
    ECA751 ECA812 BAM / bai
    ECA755 ECA812 BAM / bai
    ECA759 ECA812 BAM / bai
    ECA761 ECA812 BAM / bai
    ECA762 ECA812 BAM / bai
    ECA771 ECA812 BAM / bai
    ECA773 ECA812 BAM / bai
    ECA774 ECA812 BAM / bai
    ECA775 ECA812 BAM / bai
    ECA776 ECA812 BAM / bai
    ECA782 ECA812 BAM / bai
    ECA783 ECA812 BAM / bai
    ECA786 ECA812 BAM / bai
    ECA787 ECA812 BAM / bai
    ECA809 ECA812 BAM / bai
    ECA813 ECA812 BAM / bai
    ECA1220 ECA812 BAM / bai
    ECA1221 ECA812 BAM / bai
ECA923 ECA923 BAM / bai
    ECA922 ECA923 BAM / bai
    ECA924 ECA923 BAM / bai
    ECA925 ECA923 BAM / bai
    ECA927 ECA923 BAM / bai
ECA928 ECA928 BAM / bai
    ECA926 ECA928 BAM / bai
ECA930 ECA930 BAM / bai
ED3005 ED3005 BAM / bai
    ED3021 ED3005
ED3011 ED3011 BAM / bai
ED3012 ED3012 BAM / bai
    ED3010 ED3012
    ED3014 ED3012
    ED3015 ED3012
    ED3023 ED3012
    ED3024 ED3012
    ED3028 ED3012
ED3017 ED3017 BAM / bai
    ED3019 ED3017
    ED3020 ED3017
ED3040 ED3040 BAM / bai
ED3046 ED3046 BAM / bai
ED3048 ED3048 BAM / bai
    ED3042 ED3048
ED3049 ED3049 BAM / bai
ED3052 ED3052 BAM / bai
    ED3043 ED3052
ED3073 ED3073 BAM / bai
    ED3057 ED3073
    ED3072 ED3073
    ED3075 ED3073
    ECA571 ED3073 BAM / bai
    ECA572 ED3073 BAM / bai
ED3077 ED3077 BAM / bai
EG4347 EG4347 BAM / bai
    EG4346 EG4347
EG4349 EG4349 BAM / bai
    EG4348 EG4349
EG4724 EG4724 BAM / bai
EG4725 EG4725 BAM / bai
EG4946 EG4946 BAM / bai
    EG4680 EG4946
    EG4689 EG4946
    EG4945 EG4946
    EG4948 EG4946
    EG4951 EG4946
    EG4957 EG4946
GXW1 GXW1 BAM / bai
JT11398 JT11398 BAM / bai
    JT11362 JT11398
    JT11399 JT11398
JU1088 JU1088 BAM / bai
JU1172 JU1172 BAM / bai
JU1200 JU1200 BAM / bai
    JU2860 JU1200 BAM / bai
JU1212 JU1212 BAM / bai
    JU1207 JU1212
    JU1214 JU1212
JU1213 JU1213 BAM / bai
    JU1482 JU1213
    JU531 JU1213
    JU533 JU1213
    JU1656 JU1213 BAM / bai
    JU1762 JU1213 BAM / bai
    JU1770 JU1213 BAM / bai
JU1242 JU1242 BAM / bai
    JU1218 JU1242
    JU1230 JU1242
    JU1243 JU1242
JU1246 JU1246 BAM / bai
JU1249 JU1249 BAM / bai
JU1395 JU1395 BAM / bai
    ECA589 JU1395 BAM / bai
JU1400 JU1400 BAM / bai
JU1409 JU1409 BAM / bai
    JU1401 JU1409
    JU1410 JU1409
    JU1411 JU1409
JU1440 JU1440 BAM / bai
    JU3133 JU1440 BAM / bai
JU1491 JU1491 BAM / bai
    JU1484 JU1491
JU1530 JU1530 BAM / bai
    ECA616 JU1530 BAM / bai
JU1543 JU1543 BAM / bai
JU1568 JU1568 BAM / bai
    JU1566 JU1568
JU1581 JU1581 BAM / bai
    JU1516 JU1581 BAM / bai
    JU1522 JU1581
    JU1582 JU1581
    ECA615 JU1581 BAM / bai
    JU1807 JU1581 BAM / bai
    JU1941 JU1581 BAM / bai
JU1586 JU1586 BAM / bai
JU1652 JU1652 BAM / bai
JU1666 JU1666 BAM / bai
    JU3139 JU1666 BAM / bai
JU1792 JU1792 BAM / bai
JU1793 JU1793 BAM / bai
    JU1920 JU1793 BAM / bai
    JU1922 JU1793 BAM / bai
    JU1929 JU1793 BAM / bai
    JU2139 JU1793 BAM / bai
    JU2604 JU1793 BAM / bai
    JU2605 JU1793 BAM / bai
    JU3271 JU1793 BAM / bai
    JU1580 JU1793 BAM / bai
    JU1931 JU1793 BAM / bai
    JU3398 JU1793 BAM / bai
    JU3399 JU1793 BAM / bai
    JU3400 JU1793 BAM / bai
    JU3401 JU1793 BAM / bai
    JU3402 JU1793 BAM / bai
    JU3403 JU1793 BAM / bai
JU1808 JU1808 BAM / bai
JU1896 JU1896 BAM / bai
JU1934 JU1934 BAM / bai
JU2001 JU2001 BAM / bai
JU2007 JU2007 BAM / bai
JU2016 JU2016 BAM / bai
JU2017 JU2017 BAM / bai
JU2106 JU2106 BAM / bai
JU2131 JU2131 BAM / bai
JU2141 JU2141 BAM / bai
JU2234 JU2234 BAM / bai
JU2250 JU2250 BAM / bai
JU2257 JU2257 BAM / bai
    JU2287 JU2257 BAM / bai
JU2316 JU2316 BAM / bai
JU2464 JU2464 BAM / bai
    JU2467 JU2464 BAM / bai
    JU2468 JU2464 BAM / bai
JU2466 JU2466 BAM / bai
JU2478 JU2478 BAM / bai
JU2513 JU2513 BAM / bai
JU2519 JU2519 BAM / bai
JU2522 JU2522 BAM / bai
JU2526 JU2526 BAM / bai
JU2534 JU2534 BAM / bai
JU2565 JU2565 BAM / bai
JU2566 JU2566 BAM / bai
JU2570 JU2570 BAM / bai
JU2572 JU2572 BAM / bai
JU2575 JU2575 BAM / bai
JU2576 JU2576 BAM / bai
JU2578 JU2578 BAM / bai
JU258 JU258 BAM / bai
JU2581 JU2581 BAM / bai
JU2586 JU2586 BAM / bai
JU2587 JU2587 BAM / bai
JU2592 JU2592 BAM / bai
JU2593 JU2593 BAM / bai
JU2600 JU2600 BAM / bai
    JU1924 JU2600 BAM / bai
    JU2151 JU2600 BAM / bai
    JU3138 JU2600 BAM / bai
    JU1926 JU2600 BAM / bai
JU2610 JU2610 BAM / bai
JU2619 JU2619 BAM / bai
JU2800 JU2800 BAM / bai
    JU2802 JU2800 BAM / bai
JU2811 JU2811 BAM / bai
JU2825 JU2825 BAM / bai
JU2829 JU2829 BAM / bai
    JU2828 JU2829 BAM / bai
    JU2830 JU2829 BAM / bai
JU2838 JU2838 BAM / bai
JU2841 JU2841 BAM / bai
JU2853 JU2853 BAM / bai
JU2862 JU2862 BAM / bai
JU2866 JU2866 BAM / bai
JU2878 JU2878 BAM / bai
JU2879 JU2879 BAM / bai
JU2906 JU2906 BAM / bai
JU2907 JU2907 BAM / bai
    JU2908 JU2907 BAM / bai
JU310 JU310 BAM / bai
    JU1026 JU310
    JU1037 JU310
    JU1039 JU310
    JU1040 JU310
    JU1204 JU310
    JU1206 JU310
    JU262 JU310
    JU263 JU310
    JU299 JU310
    JU300 JU310
    JU301 JU310
    JU302 JU310
    JU303 JU310
    JU305 JU310
    JU306 JU310
    JU307 JU310
    JU309 JU310
    JU438 JU310
JU311 JU311 BAM / bai
    JU312 JU311 BAM / bai
    JU313 JU311
    JU314 JU311
    JU315 JU311 BAM / bai
    JU316 JU311
    JU317 JU311
    JU318 JU311
    JU319 JU311
    JU321 JU311
    ECA551 JU311 BAM / bai
    MY2481 JU311 BAM / bai
JU3125 JU3125 BAM / bai
JU3127 JU3127 BAM / bai
JU3128 JU3128 BAM / bai
JU3132 JU3132 BAM / bai
JU3134 JU3134 BAM / bai
JU3135 JU3135 BAM / bai
JU3137 JU3137 BAM / bai
JU3140 JU3140 BAM / bai
JU3141 JU3141 BAM / bai
JU3144 JU3144 BAM / bai
JU3166 JU3166 BAM / bai
JU3167 JU3167 BAM / bai
JU3169 JU3169 BAM / bai
JU3224 JU3224 BAM / bai
JU3225 JU3225 BAM / bai
JU3226 JU3226 BAM / bai
JU3228 JU3228 BAM / bai
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JU323 JU323 BAM / bai
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JU3280 JU3280 BAM / bai
JU3282 JU3282 BAM / bai
JU3291 JU3291 BAM / bai
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JU367 JU367 BAM / bai
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JU393 JU393 BAM / bai
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JU406 JU406 BAM / bai
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JU440 JU440 BAM / bai
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JU830 JU830 BAM / bai
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JU847 JU847 BAM / bai
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KR314 KR314 BAM / bai
LKC34 LKC34 BAM / bai
MY1 MY1 BAM / bai
MY10 MY10 BAM / bai
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MY16 MY16 BAM / bai
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MY2147 MY2147 BAM / bai
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MY518 MY518 BAM / bai
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N2 N2 BAM / bai
    ECA253 N2 BAM / bai
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    ECA255 N2
    ECA257 N2
NIC1 NIC1 BAM / bai
NIC1049 NIC1049 BAM / bai
NIC1107 NIC1107 BAM / bai
NIC1119 NIC1119 BAM / bai
NIC166 NIC166 BAM / bai
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NIC195 NIC195 BAM / bai
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NIC2 NIC2 BAM / bai
NIC207 NIC207 BAM / bai
NIC231 NIC231 BAM / bai
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NIC236 NIC236 BAM / bai
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NIC242 NIC242 BAM / bai
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NIC262 NIC262 BAM / bai
NIC265 NIC265 BAM / bai
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NIC267 NIC267 BAM / bai
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NIC268 NIC268 BAM / bai
NIC269 NIC269 BAM / bai
NIC271 NIC271 BAM / bai
NIC272 NIC272 BAM / bai
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NIC274 NIC274 BAM / bai
NIC275 NIC275 BAM / bai
NIC276 NIC276 BAM / bai
NIC277 NIC277 BAM / bai
NIC3 NIC3 BAM / bai
    NIC4 NIC3 BAM / bai
NIC501 NIC501 BAM / bai
NIC511 NIC511 BAM / bai
NIC513 NIC513 BAM / bai
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NIC528 NIC528 BAM / bai
NIC529 NIC529 BAM / bai
PB303 PB303 BAM / bai
ECA259 PB306 BAM / bai
    ECA258 PB306
PS2025 PS2025 BAM / bai
PX179 PX179 BAM / bai
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QG2075 QG2075 BAM / bai
QG2811 QG2811 BAM / bai
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QG2874 QG2874 BAM / bai
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QG536 QG536 BAM / bai
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QG556 QG556 BAM / bai
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QG557 QG557 BAM / bai
QW947 QW947 BAM / bai
QX1211 QX1211 BAM / bai
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QX1791 QX1791 BAM / bai
QX1792 QX1792 BAM / bai
QX1793 QX1793 BAM / bai
QX1794 QX1794 BAM / bai
RC301 RC301 BAM / bai
    MY2022 RC301 BAM / bai
    MY2024 RC301 BAM / bai
    MY2078 RC301 BAM / bai
    MY2291 RC301 BAM / bai
    MY2630 RC301 BAM / bai
    MY2636 RC301 BAM / bai
    MY2640 RC301 BAM / bai
    MY2681 RC301 BAM / bai
    MY2684 RC301 BAM / bai
    MY2691 RC301 BAM / bai
    MY684 RC301 BAM / bai
    MY882 RC301 BAM / bai
TWN2530 TWN2530 BAM / bai
TWN2542 TWN2542 BAM / bai
    TWN2794 TWN2542 BAM / bai
    TWN2803 TWN2542 BAM / bai
WN2001 WN2001 BAM / bai
    WN2010 WN2001 BAM / bai
    WN2011 WN2001 BAM / bai
    WN2013 WN2001 BAM / bai
    WN2014 WN2001 BAM / bai
    WN2016 WN2001 BAM / bai
    WN2017 WN2001 BAM / bai
    WN2018 WN2001 BAM / bai
    WN2019 WN2001 BAM / bai
    WN2020 WN2001 BAM / bai
    WN2021 WN2001 BAM / bai
WN2002 WN2002 BAM / bai
    WN2003 WN2002
WN2033 WN2033 BAM / bai
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WN2050 WN2050 BAM / bai
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WN2063 WN2063 BAM / bai
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    WN2075 WN2066 BAM / bai
WN2068 WN2068 BAM / bai
    WN2071 WN2068 BAM / bai
WN2069 WN2069 BAM / bai
XZ1513 XZ1513 BAM / bai
    XZ2212 XZ1513 BAM / bai
XZ1514 XZ1514 BAM / bai
XZ1515 XZ1515 BAM / bai
XZ1516 XZ1516 BAM / bai
XZ1672 XZ1672 BAM / bai
XZ1734 XZ1734 BAM / bai
XZ1735 XZ1735 BAM / bai
XZ1756 XZ1756 BAM / bai
XZ2018 XZ2018 BAM / bai
XZ2019 XZ2019 BAM / bai
XZ2020 XZ2020 BAM / bai
XZ2211 XZ2211 BAM / bai
Strain Issues
CB3191 Identical to N2, McGrath et al. 2009
CB3192 Identical to N2, McGrath et al. 2009
CB3193 Identical to N2, McGrath et al. 2009
CB3194 Identical to N2, McGrath et al. 2009
CB3195 Identical to N2, McGrath et al. 2009
CB4507 Identical to N2, McGrath et al. 2009, Likely dauer mutant from N2 screen
CB4555 N2xCB4851 recombinant, misfrozen as a wild isolate, McGrath et al. 2009
DH424 N2xCB4851 recombinant, misfrozen as a wild isolate, McGrath et al. 2009
DR1349 N2xCB4851 recombinant, misfrozen as a wild isolate, McGrath et al. 2009
ECA244 WGS identical to N2
ECA252 By WGS, this strain is a recombinant between N2 and CB4851.
LSJ1 Strain derivative highly related to N2 but cultured in high-density liquid culture, not a wild isolate
PX174 WGS shows identity with RC301, Andersen et al. 2012
PX176 Identical to N2, McGrath et al. 2009
TR388 Identical to N2, McGrath et al. 2009
TR389 Identical to N2, McGrath et al. 2009
TR403 N2xCB4851 recombinant, misfrozen as a wild isolate, McGrath et al. 2009
ECA339 By WGS, this strain is the same as ECA252. It is a recombinant between N2 and CB4851.
JU1893 WGS aligns as C. briggsae
JU2461 WGS aligns as C. briggsae
JU2574 WGS aligns as C. briggsae
JU2771 WGS aligns as C. briggsae
ECA1219 WGS shows that this strain is identical to N2

Methods / Pipelines

This tab links to the nextflow pipelines used to process wild isolate sequence data.

FASTQ QC and Trimming

andersenlab/trim-fq-nf -- (Latest f0b63e)

Adapters and low quality sequences were trimmed off of raw reads using fastp (0.20.0) and default parameters. Reads shorter than 20 bp after trimming were discarded.

Alignment

andersenlab/alignment-nf -- (892b37)

Trimmed reads were aligned to C. elegans reference genome (project PRJNA13758 version WS276 from the Wormbase) using bwa mem BWA (0.7.17). Libraries of the same strain were merged together and indexed by sambamba (0.7.0). Duplicates were flagged with Picard (2.21.3).

Strains with less than 14x coverage were not included in the alignment report and subsequent analyses.

Variant Calling

andersenlab/wi-gatk -- (c9dd1e)

Variants for each strain were called using gatk HaplotypeCaller. After the initial variant calling, variants were combined and then recalled jointly using gatk GenomicsDBImport and gatk GenotypeGVCFs GATK (4.1.4.0).

The variants were further processed and filtered with custom-written scripts for heterozygous SNV polarization, GATK (4.1.4.0), and bcftools (1.10).

Warning
Heterozygous polarization and filtering thresholds were optimized for single nucleotide variants (SNVs).

Additionally, insertion or deletion (indel) variants less than 50 bp are more reliably called than indel variants greater than this size. In general, indel variants should be considered less reliable than SNVs.

Site-level filtering and annotation

  1. Heterozygous SNV polarization: Because C. elegans is a selfing species, heterozygous SNV sites are most likely errors. Biallelic heterozygous SNVs were converted to homozygous REF or ALT if we had sufficient evidence for conversion. Only biallelic SNVs that are not on mitochondria DNA were included in this step. Specifically, the SNV was converted if the normalized Phred-scaled likelihoods (PL) met the following criteria (a smaller PL means more confidence). Any heterozygous SNVs that did not meet these criteria were left unchanged.

    • If PL-ALT/PL-REF <= 0.5 and PL-ALT <= 200, convert to homozygous ALT
    • If PL-REF/PL-ALT <= 0.5 and PL-REF <= 200, convert to homozygous REF
  2. Soft filtering: Low quality sites were flagged but not modified or removed.

    For the site-level soft filter, variant sites that meet the following conditions were flagged as PASS. These stats were computed across all samples for each site.

    • Variant quality (QUAL) > 30 (this filter is very lenient, only three sites failed)
    • Variant quality normalized by read depth (QD) > 20
    • Strand bias of ALT calls: strand odds ratio (SOR) < 5
    • Strand bias of ALT calls: Fisherstrand (FS) < 100
    • Fraction of samples with missing genotype < 95%
    • Fraction of samples with heterozygous genotype after heterozygous site polarization < 10%

    For the sample-level soft filter, genotypes that meet the following filters were flagged as PASS for each site in each sample:

    • Read depth (DP) > 5
    • Site is not heterozygous
  3. SnpEff Annotation: The predicted impact of each variant site was annotated with SnpEff (4.3.1t).

  4. For the hard-filtered VCF, low quality sites were modified or removed using the following criteria.

    • For the site-level hard filter, variant sites not flagged as PASS were removed.
    • For the sample-level hard filter, genotypes not flagged as PASS were converted to missing (./.), with the exception that heterozygous sites on mitochondria where kept unchanged.

    After the steps above, sites that are invariant (0/0 or 1/1 across all samples, not counting missing ./.) were removed.

  5. Variant impacts were then annotated using bcftools csq, which takes into consideration nearby variants and annotates variant impacts based on haplotypes.

Determination of filter thresholds

We re-examined our filter thresholds for this release. A variant simulation pipeline was used as part of this process:

Please see the filter optimization report for further details.

Isotype Assignment

andersenlab/concordance-nf -- (ae3d80)

Isotype groups contain strains that are likely identical to each other and were sampled from the same isolation locations. For any phenotypic assay, only the isotype reference strain needs to be scored. Users interested in individual strain genotypes can use the strain-level data.

Strains were grouped into isotypes using the following steps:

  1. Using all high quality variants (the hard-filtered VCF) and bcftools gtcheck, concordance for each pair of strains was calculated as a fraction of shared variants over the total variants in each pair.

  2. Strain pairs with concordance > 0.9995 were grouped into the same isotype group. The threshold 0.9995 was determined by:

    • Examining the distribution of concordance scores.
    • Capturing similarity between strains to minimize the number of strains that get assigned to multiple isotype groups.
    • Agreement with the isotype groups in previous releases.
  3. The following issues, which were rare, were resolved on a case-by-case basis:

    • If one strain was assigned to multiple isotypes.
    • If one isotype from previous releases matches to multiple new isotype groups.
    • If one new isotype group contains strains from multiple isotypes from previous releases.

When issues arose, the pairwise concordance between all strains within an isotype were examined manually. Strains and isotypes may be re-assigned with the goal that strains within the same isotype group should have high concordance with each other, and strains from different isotype groups should have lower concordance.

Tree Generation

Trees were generated by converting the hard-filtered VCF to Phylip format using vcf2phylip (030b8d). Then, the Phylip format was converted to Stockholm format using Bioconvert (0.3.0), which was then used to construct a tree with QuickTree (2.5) using default settings. The trees were plotted with FigTree (1.4.4) rooting on the most diverse strain XZ1516.

Imputation

Imputation was done using Beagle (5.1) with the following parameters: window=5 overlap=2 (except for chromosome X, which used window=3 overlap=1 to run with available memory) impute=true ne=100000 imp-segment=0.5 imp-step=0.01 cluster=0.0005.