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Genomic Data

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Release Summary
  • Strains: 331
  • WGS strains: 192
  • Isotypes: 152
  • Genome: WS245

Alignment Data

Wild isolate genomes are aligned and stored using the BAM format. BAMs are available in the table below.

Downloading All Alignment Data

You can download all alignment data using the script below. Before this script will work, you need to download and install wget. We recommend using Homebrew for this installation (Unix/Mac OS), or Cygwin on windows. See the FAQ for details on installing wget.

download_bams.sh

Methods

Information regarding alignment, variant calling, and annotation are available here.

Variant Data

We used samtools to identify single-nucleotide variant (SNV) sites as compared to the N2 reference genome. Variant data are provided as VCF or tab-delimited files.

VCF

VCFs generated from the variant calling pipeline are provided below.

  • Soft-filter - Includes all variants and annotations. The QC status of variants is included.
  • Hard-filter - Variants and genotypes that fail QC are removed.
  • Imputed - An imputed dataset generated from the hard-filter VCF.

You can programmatically access specific regions of VCF files (rather then the entire file) from the command line:


Strain Data
Strain Data including isolation location, isotype information, and more is available for download.

Download Strain Data

Included Variants

Currently, we have performed variant calling across all wild isolates. We are working to add additional variant classes including insertion/deletion, structural, transposon, and additional variant classes.

Transposon Data

We have recently performed an analysis characterizing Transposon variation in C. elegans. The dataset will be further integrated with the site resources as time goes on. For now, the raw data are available below.

Download Transposon Data
# Reference Strain Isotype Strains Isotype BAM Tab-delimited variants
1 AB1 AB1 AB1 BAM / BAI AB1.20160408.tsv
2 BRC20067 BRC20067 BRC20067 BAM / BAI BRC20067.20160408.tsv
3 ECA243 CB4851 DR1344 ECA243 RW7000 BAM / BAI CB4851.20160408.tsv
4 CB4852 CB4852 CB4852 JU1563 BAM / BAI CB4852.20160408.tsv
5 ECA246 CB4853 CB3198 DR1350 ECA245 ECA246 BAM / BAI CB4853.20160408.tsv
6 CB4854 CB4854 CB3196 CB3197 CB4854 BAM / BAI CB4854.20160408.tsv
7 ECA248 CB4855 ECA248 BAM / BAI CB4855.20160408.tsv
8 CB4856 CB4856 CB4856 ECA260 BAM / BAI CB4856.20160408.tsv
9 ECA250 CB4857 CB3199 DR1345 ECA249 ECA250 BAM / BAI CB4857.20160408.tsv
10 ECA251 CB4858 AB2 AB4 CX11258 CX11278 CX11305 CX11317 ECA247 ECA251 BAM / BAI CB4858.20160408.tsv
11 CB4932 CB4932 CB4932 BAM / BAI CB4932.20160408.tsv
12 CX11254 CX11254 CX11254 BAM / BAI CX11254.20160408.tsv
13 CX11262 CX11262 CX11262 CX11294 BAM / BAI CX11262.20160408.tsv
14 CX11264 CX11264 CX11264 BAM / BAI CX11264.20160408.tsv
15 CX11271 CX11271 CX11271 CX11319 BAM / BAI CX11271.20160408.tsv
16 CX11276 CX11276 CX11276 CX11316 BAM / BAI CX11276.20160408.tsv
17 CX11285 CX11285 CX11285 CX11321 BAM / BAI CX11285.20160408.tsv
18 CX11292 CX11292 CX11259 CX11292 BAM / BAI CX11292.20160408.tsv
19 CX11307 CX11307 CX11307 BAM / BAI CX11307.20160408.tsv
20 CX11314 CX11314 CX11314 BAM / BAI CX11314.20160408.tsv
21 CX11315 CX11315 CX11268 CX11315 BAM / BAI CX11315.20160408.tsv
22 DL200 DL200 DL200 BAM / BAI DL200.20160408.tsv
23 DL226 DL226 DL226 BAM / BAI DL226.20160408.tsv
24 DL238 DL238 DL238 BAM / BAI DL238.20160408.tsv
25 ECA36 ECA36 ECA36 BAM / BAI ECA36.20160408.tsv
26 ED3005 ED3005 ED3005 ED3021 BAM / BAI ED3005.20160408.tsv
27 ED3011 ED3011 ED3011 BAM / BAI ED3011.20160408.tsv
28 ED3012 ED3012 ED3010 ED3012 ED3014 ED3015 ED3023 ED3024 ED3028 BAM / BAI ED3012.20160408.tsv
29 ED3017 ED3017 ED3017 ED3019 ED3020 BAM / BAI ED3017.20160408.tsv
30 ED3040 ED3040 ED3040 BAM / BAI ED3040.20160408.tsv
31 ED3046 ED3046 ED3046 BAM / BAI ED3046.20160408.tsv
32 ED3048 ED3048 ED3042 ED3048 BAM / BAI ED3048.20160408.tsv
33 ED3049 ED3049 ED3049 BAM / BAI ED3049.20160408.tsv
34 ED3052 ED3052 ED3043 ED3052 BAM / BAI ED3052.20160408.tsv
35 ED3073 ED3073 ED3057 ED3072 ED3073 ED3075 BAM / BAI ED3073.20160408.tsv
36 ED3077 ED3077 ED3077 BAM / BAI ED3077.20160408.tsv
37 EG4347 EG4347 EG4346 EG4347 BAM / BAI EG4347.20160408.tsv
38 EG4349 EG4349 EG4348 EG4349 BAM / BAI EG4349.20160408.tsv
39 EG4724 EG4724 EG4724 BAM / BAI EG4724.20160408.tsv
40 EG4725 EG4725 EG4725 BAM / BAI EG4725.20160408.tsv
41 EG4946 EG4946 EG4680 EG4689 EG4945 EG4946 EG4948 EG4951 EG4957 BAM / BAI EG4946.20160408.tsv
42 GXW1 GXW1 GXW1 BAM / BAI GXW1.20160408.tsv
43 JT11398 JT11398 JT11362 JT11398 JT11399 BAM / BAI JT11398.20160408.tsv
44 JU1088 JU1088 JU1088 BAM / BAI JU1088.20160408.tsv
45 JU1172 JU1172 JU1172 BAM / BAI JU1172.20160408.tsv
46 JU1200 JU1200 JU1200 BAM / BAI JU1200.20160408.tsv
47 JU1212 JU1212 JU1207 JU1212 JU1214 BAM / BAI JU1212.20160408.tsv
48 JU1213 JU1213 JU1213 JU1482 JU531 JU533 BAM / BAI JU1213.20160408.tsv
49 JU1242 JU1242 JU1218 JU1230 JU1242 JU1243 BAM / BAI JU1242.20160408.tsv
50 JU1246 JU1246 JU1246 BAM / BAI JU1246.20160408.tsv
51 JU1395 JU1395 ECA589 JU1395 BAM / BAI JU1395.20160408.tsv
52 JU1400 JU1400 JU1400 BAM / BAI JU1400.20160408.tsv
53 JU1409 JU1409 JU1401 JU1409 JU1410 JU1411 BAM / BAI JU1409.20160408.tsv
54 JU1440 JU1440 JU1440 BAM / BAI JU1440.20160408.tsv
55 JU1491 JU1491 JU1484 JU1491 BAM / BAI JU1491.20160408.tsv
56 JU1530 JU1530 ECA616 JU1530 BAM / BAI JU1530.20160408.tsv
57 JU1568 JU1568 JU1566 JU1568 BAM / BAI JU1568.20160408.tsv
58 JU1581 JU1581 JU1516 JU1522 JU1581 JU1582 BAM / BAI JU1581.20160408.tsv
59 JU1586 JU1586 JU1586 BAM / BAI JU1586.20160408.tsv
60 JU1652 JU1652 JU1652 BAM / BAI JU1652.20160408.tsv
61 JU1896 JU1896 JU1896 BAM / BAI JU1896.20160408.tsv
62 JU2001 JU2001 JU2001 BAM / BAI JU2001.20160408.tsv
63 JU2007 JU2007 JU2007 BAM / BAI JU2007.20160408.tsv
64 JU2316 JU2316 JU2316 BAM / BAI JU2316.20160408.tsv
65 JU2464 JU2464 JU2464 JU2467 JU2468 BAM / BAI JU2464.20160408.tsv
66 JU2466 JU2466 JU2466 BAM / BAI JU2466.20160408.tsv
67 JU2513 JU2513 JU2513 BAM / BAI JU2513.20160408.tsv
68 JU2519 JU2519 JU2519 BAM / BAI JU2519.20160408.tsv
69 JU2522 JU2522 JU2522 BAM / BAI JU2522.20160408.tsv
70 JU2526 JU2526 JU2526 BAM / BAI JU2526.20160408.tsv
71 JU258 JU258 JU258 BAM / BAI JU258.20160408.tsv
72 JU310 JU310 JU1026 JU1037 JU1039 JU1040 JU1204 JU1206 JU262 JU263 JU299 JU300 JU301 JU302 JU303 JU305 JU306 JU307 JU309 JU310 JU438 BAM / BAI JU310.20160408.tsv
73 JU311 JU311 JU311 JU312 JU313 JU314 JU315 JU316 JU317 JU318 JU319 JU321 BAM / BAI JU311.20160408.tsv
74 JU323 JU323 JU322 JU323 JU342 JU347 BAM / BAI JU323.20160408.tsv
75 JU346 JU346 JU346 BAM / BAI JU346.20160408.tsv
76 JU360 JU360 JU360 JU362 JU363 JU364 JU366 JU368 JU369 JU370 JU801 BAM / BAI JU360.20160408.tsv
77 JU367 JU367 JU361 JU367 JU371 JU692 JU693 JU694 BAM / BAI JU367.20160408.tsv
78 JU393 JU393 JU393 BAM / BAI JU393.20160408.tsv
79 JU394 JU394 JU394 JU399 JU400 BAM / BAI JU394.20160408.tsv
80 JU397 JU397 JU397 JU398 JU401 JU402 BAM / BAI JU397.20160408.tsv
81 JU406 JU406 JU406 JU407 BAM / BAI JU406.20160408.tsv
82 JU440 JU440 JU440 BAM / BAI JU440.20160408.tsv
83 JU561 JU561 JU561 JU563 BAM / BAI JU561.20160408.tsv
84 JU642 JU642 JU642 BAM / BAI JU642.20160408.tsv
85 JU751 JU751 JU751 BAM / BAI JU751.20160408.tsv
86 JU774 JU774 JU774 BAM / BAI JU774.20160408.tsv
87 JU775 JU775 JU775 JU799 BAM / BAI JU775.20160408.tsv
88 JU778 JU778 JU778 BAM / BAI JU778.20160408.tsv
89 JU782 JU782 JU782 BAM / BAI JU782.20160408.tsv
90 JU792 JU792 JU395 JU396 JU622 JU792 BAM / BAI JU792.20160408.tsv
91 JU830 JU830 JU829 JU830 BAM / BAI JU830.20160408.tsv
92 JU847 JU847 JU847 JU848 BAM / BAI JU847.20160408.tsv
93 KR314 KR314 KR314 BAM / BAI KR314.20160408.tsv
94 LKC34 LKC34 LKC34 BAM / BAI LKC34.20160408.tsv
95 MY1 MY1 MY1 BAM / BAI MY1.20160408.tsv
96 MY10 MY10 MY17 MY10 MY11 MY12 MY13 MY19 MY20 MY21 MY22 MY3 MY4 MY5 MY7 MY8 MY9 BAM / BAI MY10.20160408.tsv
97 MY16 MY16 MY16 BAM / BAI MY16.20160408.tsv
98 MY18 MY18 MY18 MY6 BAM / BAI MY18.20160408.tsv
99 MY23 MY23 JU1171 MY14 MY15 MY2 MY23 BAM / BAI MY23.20160408.tsv
100 N2 N2 ECA253 ECA254 ECA255 ECA257 N2 BAM / BAI N2.20160408.tsv
101 NIC1 NIC1 NIC1 BAM / BAI NIC1.20160408.tsv
102 NIC166 NIC166 NIC166 BAM / BAI NIC166.20160408.tsv
103 NIC195 NIC195 NIC195 NIC196 NIC197 NIC198 BAM / BAI NIC195.20160408.tsv
104 NIC199 NIC199 NIC199 NIC200 BAM / BAI NIC199.20160408.tsv
105 NIC2 NIC2 NIC2 BAM / BAI NIC2.20160408.tsv
106 NIC207 NIC207 NIC207 BAM / BAI NIC207.20160408.tsv
107 NIC231 NIC231 NIC231 NIC232 BAM / BAI NIC231.20160408.tsv
108 NIC236 NIC236 NIC236 NIC237 BAM / BAI NIC236.20160408.tsv
109 NIC242 NIC242 NIC242 BAM / BAI NIC242.20160408.tsv
110 NIC251 NIC251 NIC251 BAM / BAI NIC251.20160408.tsv
111 NIC252 NIC252 NIC252 BAM / BAI NIC252.20160408.tsv
112 NIC255 NIC255 NIC255 BAM / BAI NIC255.20160408.tsv
113 NIC256 NIC256 NIC256 NIC263 BAM / BAI NIC256.20160408.tsv
114 NIC258 NIC258 NIC258 BAM / BAI NIC258.20160408.tsv
115 NIC259 NIC259 NIC259 BAM / BAI NIC259.20160408.tsv
116 NIC260 NIC260 NIC260 BAM / BAI NIC260.20160408.tsv
117 NIC261 NIC261 NIC261 BAM / BAI NIC261.20160408.tsv
118 NIC262 NIC262 NIC262 BAM / BAI NIC262.20160408.tsv
119 NIC265 NIC265 NIC265 BAM / BAI NIC265.20160408.tsv
120 NIC266 NIC266 NIC266 BAM / BAI NIC266.20160408.tsv
121 NIC267 NIC267 NIC267 NIC270 BAM / BAI NIC267.20160408.tsv
122 NIC268 NIC268 NIC268 BAM / BAI NIC268.20160408.tsv
123 NIC269 NIC269 NIC269 BAM / BAI NIC269.20160408.tsv
124 NIC271 NIC271 NIC271 BAM / BAI NIC271.20160408.tsv
125 NIC272 NIC272 NIC272 NIC273 BAM / BAI NIC272.20160408.tsv
126 NIC274 NIC274 NIC274 BAM / BAI NIC274.20160408.tsv
127 NIC275 NIC275 NIC275 BAM / BAI NIC275.20160408.tsv
128 NIC276 NIC276 NIC276 BAM / BAI NIC276.20160408.tsv
129 NIC277 NIC277 NIC277 BAM / BAI NIC277.20160408.tsv
130 NIC3 NIC3 NIC3 NIC4 BAM / BAI NIC3.20160408.tsv
131 PB303 PB303 PB303 BAM / BAI PB303.20160408.tsv
132 ECA259 PB306 ECA258 ECA259 BAM / BAI PB306.20160408.tsv
133 PS2025 PS2025 PS2025 BAM / BAI PS2025.20160408.tsv
134 PX179 PX179 PX178 PX179 BAM / BAI PX179.20160408.tsv
135 QG2075 QG2075 QG2075 BAM / BAI QG2075.20160408.tsv
136 QG536 QG536 QG536 QG537 QG538 BAM / BAI QG536.20160408.tsv
137 QG556 QG556 QG556 QG558 BAM / BAI QG556.20160408.tsv
138 QG557 QG557 QG557 BAM / BAI QG557.20160408.tsv
139 QW947 QW947 QW947 BAM / BAI QW947.20160408.tsv
140 QX1211 QX1211 QX1211 QX1215 QX1216 BAM / BAI QX1211.20160408.tsv
141 QX1212 QX1212 QX1212 QX1213 QX1214 BAM / BAI QX1212.20160408.tsv
142 QX1233 QX1233 QX1218 QX1233 BAM / BAI QX1233.20160408.tsv
143 QX1791 QX1791 QX1791 BAM / BAI QX1791.20160408.tsv
144 QX1792 QX1792 QX1792 BAM / BAI QX1792.20160408.tsv
145 QX1793 QX1793 QX1793 BAM / BAI QX1793.20160408.tsv
146 QX1794 QX1794 QX1794 BAM / BAI QX1794.20160408.tsv
147 RC301 RC301 RC301 BAM / BAI RC301.20160408.tsv
148 WN2001 WN2001 WN2001 WN2010 WN2011 WN2013 WN2014 WN2016 WN2017 WN2018 WN2019 WN2020 WN2021 BAM / BAI WN2001.20160408.tsv
149 WN2002 WN2002 WN2002 WN2003 BAM / BAI WN2002.20160408.tsv


The following statistics were generated with bcftools stats. The soft-filtered VCF for this release has had records and genotypes annotated but no data has been removed. The hard-filtered VCF removes records and genotypes that have been annotated with filters.

The hard-filtered VCF has stripped records and genotypes that have had filters applied.

Variable Soft-Filtered Hard-Filtered
Samples 152 152
SNVs 1,617,867 1,320,573
Ts 897,554 735,536
Tv 758,466 609,461
Ts/Tv 1.18 1.21
These numbers reflect the number of variants in the entire CeNDR C. elegans population.

Methods

Note: These methods operated on sequence data at the isotype level.

Software

Alignment

Sequences were aligned to WS245 using BWA (version 0.7.8-r455). Optical/PCR duplicates were marked with PICARD (version 1.111).

Variant Calling

SNV calling was performed using bcftools (version 1.3).

Filtering

Sites with greater than 10% missing or greater than 90% heterozygous calls across all isotypes were removed. Individual calls with the following parameters were removed:

  • Depth of coverage (DP) <= 10
  • Quality (QUAL) < 30
  • Mapping Quality (MQ) < 40. Only applied to ALT calls.
  • Number of high-quality non-reference bases (DV) / Depth of Coverage (DP) < 0.5. Applied only to ALT calls.

Annotation

Variants were annotated using SnpEff (version 4.1g) using the WS241 database.

Pipelines

The C. elegans Natural Diversity Resource has three git repos which contain the software used to run the site.

AndersenLab/cegwas

A set of functions to process phenotype data, perform GWAS, and perform post-mapping data processing for C. elegans.

AndersenLab/cegwas-worker

A python daemon that handles submitted mapping jobs from base. cegwas-worker Runs on Google Compute Engine.

AndersenLab/CeNDR

The software responsible for this website, which is run using Google App Engine.