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Genomic Data

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Release Summary
  • Strains: 552
  • WGS strains: 413
  • Isotypes: 249
  • Genome: WS258

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 AB1.20170531.tsv
2 BRC20067 BRC20067 BRC20067 BRC20113 BAM / BAI BRC20067.20170531.tsv
3 BRC20263 BRC20263 BRC20263 BAM / BAI BRC20263.20170531.tsv
4 ECA243 CB4851 DR1344 ECA243 RW7000 BAM / BAI CB4851.20170531.tsv
5 CB4852 CB4852 CB4852 JU1563 BAM / BAI CB4852.20170531.tsv
6 ECA246 CB4853 CB3198 DR1350 ECA245 ECA246 BAM / BAI CB4853.20170531.tsv
7 CB4854 CB4854 CB3196 CB3197 CB4854 BAM / BAI CB4854.20170531.tsv
8 ECA248 CB4855 ECA248 BAM / BAI CB4855.20170531.tsv
9 CB4856 CB4856 CB4856 ECA260 BAM / BAI CB4856.20170531.tsv
10 ECA250 CB4857 CB3199 DR1345 ECA249 ECA250 BAM / BAI CB4857.20170531.tsv
11 ECA251 CB4858 AB2 AB4 CX11258 CX11278 CX11305 CX11317 ECA247 ECA251 JU1960 BAM / BAI CB4858.20170531.tsv
12 CB4932 CB4932 CB4932 BAM / BAI CB4932.20170531.tsv
13 CX11254 CX11254 CX11254 BAM / BAI CX11254.20170531.tsv
14 CX11262 CX11262 CX11262 CX11294 BAM / BAI CX11262.20170531.tsv
15 CX11264 CX11264 CX11264 BAM / BAI CX11264.20170531.tsv
16 CX11271 CX11271 CX11271 CX11319 BAM / BAI CX11271.20170531.tsv
17 CX11276 CX11276 CX11276 CX11316 BAM / BAI CX11276.20170531.tsv
18 CX11285 CX11285 CX11285 CX11321 BAM / BAI CX11285.20170531.tsv
19 CX11292 CX11292 CX11259 CX11292 BAM / BAI CX11292.20170531.tsv
20 CX11307 CX11307 CX11307 BAM / BAI CX11307.20170531.tsv
21 CX11314 CX11314 CX11314 BAM / BAI CX11314.20170531.tsv
22 CX11315 CX11315 CX11268 CX11315 BAM / BAI CX11315.20170531.tsv
23 DL200 DL200 DL200 BAM / BAI DL200.20170531.tsv
24 DL226 DL226 DL226 BAM / BAI DL226.20170531.tsv
25 DL238 DL238 DL238 BAM / BAI DL238.20170531.tsv
26 ECA189 ECA189 ECA189 ECA190 ECA192 ECA193 ECA393 ECA395 BAM / BAI ECA189.20170531.tsv
27 ECA191 ECA191 ECA191 BAM / BAI ECA191.20170531.tsv
28 ECA348 ECA348 ECA348 BAM / BAI ECA348.20170531.tsv
29 ECA349 ECA349 ECA349 ECA350 BAM / BAI ECA349.20170531.tsv
30 ECA36 ECA36 ECA36 BAM / BAI ECA36.20170531.tsv
31 ECA363 ECA363 ECA363 BAM / BAI ECA363.20170531.tsv
32 ECA369 ECA369 ECA369 BAM / BAI ECA369.20170531.tsv
33 ECA372 ECA372 ECA372 BAM / BAI ECA372.20170531.tsv
34 ECA396 ECA396 ECA396 ECA397 ECA398 ECA399 BAM / BAI ECA396.20170531.tsv
35 ED3005 ED3005 ED3005 ED3021 BAM / BAI ED3005.20170531.tsv
36 ED3011 ED3011 ED3011 BAM / BAI ED3011.20170531.tsv
37 ED3012 ED3012 ED3010 ED3012 ED3014 ED3015 ED3023 ED3024 ED3028 BAM / BAI ED3012.20170531.tsv
38 ED3017 ED3017 ED3017 ED3019 ED3020 BAM / BAI ED3017.20170531.tsv
39 ED3040 ED3040 ED3040 BAM / BAI ED3040.20170531.tsv
40 ED3046 ED3046 ED3046 BAM / BAI ED3046.20170531.tsv
41 ED3048 ED3048 ED3042 ED3048 BAM / BAI ED3048.20170531.tsv
42 ED3049 ED3049 ED3049 BAM / BAI ED3049.20170531.tsv
43 ED3052 ED3052 ED3043 ED3052 BAM / BAI ED3052.20170531.tsv
44 ED3073 ED3073 ED3057 ED3072 ED3073 ED3075 BAM / BAI ED3073.20170531.tsv
45 ED3077 ED3077 ED3077 BAM / BAI ED3077.20170531.tsv
46 EG4347 EG4347 EG4346 EG4347 BAM / BAI EG4347.20170531.tsv
47 EG4349 EG4349 EG4348 EG4349 BAM / BAI EG4349.20170531.tsv
48 EG4724 EG4724 EG4724 BAM / BAI EG4724.20170531.tsv
49 EG4725 EG4725 EG4725 BAM / BAI EG4725.20170531.tsv
50 EG4946 EG4946 EG4680 EG4689 EG4945 EG4946 EG4948 EG4951 EG4957 BAM / BAI EG4946.20170531.tsv
51 GXW1 GXW1 GXW1 BAM / BAI GXW1.20170531.tsv
52 JT11398 JT11398 JT11362 JT11398 JT11399 BAM / BAI JT11398.20170531.tsv
53 JU1088 JU1088 JU1088 BAM / BAI JU1088.20170531.tsv
54 JU1172 JU1172 JU1172 BAM / BAI JU1172.20170531.tsv
55 JU1200 JU1200 JU1200 JU2860 BAM / BAI JU1200.20170531.tsv
56 JU1212 JU1212 JU1207 JU1212 JU1214 BAM / BAI JU1212.20170531.tsv
57 JU1213 JU1213 JU1213 JU1482 JU1656 JU1762 JU1770 JU531 JU533 BAM / BAI JU1213.20170531.tsv
58 JU1242 JU1242 JU1218 JU1230 JU1242 JU1243 BAM / BAI JU1242.20170531.tsv
59 JU1246 JU1246 JU1246 BAM / BAI JU1246.20170531.tsv
60 JU1249 JU1249 JU1249 BAM / BAI JU1249.20170531.tsv
61 JU1395 JU1395 ECA589 JU1395 BAM / BAI JU1395.20170531.tsv
62 JU1400 JU1400 JU1400 BAM / BAI JU1400.20170531.tsv
63 JU1409 JU1409 JU1401 JU1409 JU1410 JU1411 BAM / BAI JU1409.20170531.tsv
64 JU1440 JU1440 JU1440 JU3133 BAM / BAI JU1440.20170531.tsv
65 JU1491 JU1491 JU1484 JU1491 BAM / BAI JU1491.20170531.tsv
66 JU1530 JU1530 ECA616 JU1530 BAM / BAI JU1530.20170531.tsv
67 JU1543 JU1543 JU1543 BAM / BAI JU1543.20170531.tsv
68 JU1568 JU1568 JU1566 JU1568 BAM / BAI JU1568.20170531.tsv
69 JU1581 JU1581 ECA615 JU1516 JU1522 JU1581 JU1582 JU1807 BAM / BAI JU1581.20170531.tsv
70 JU1586 JU1586 JU1586 BAM / BAI JU1586.20170531.tsv
71 JU1652 JU1652 JU1652 BAM / BAI JU1652.20170531.tsv
72 JU1666 JU1666 JU1666 JU3139 BAM / BAI JU1666.20170531.tsv
73 JU1792 JU1792 JU1792 BAM / BAI JU1792.20170531.tsv
74 JU1793 JU1793 JU1793 JU1920 JU1922 JU1929 JU2139 JU2604 JU2605 BAM / BAI JU1793.20170531.tsv
75 JU1808 JU1808 JU1808 BAM / BAI JU1808.20170531.tsv
76 JU1896 JU1896 JU1896 BAM / BAI JU1896.20170531.tsv
77 JU1934 JU1934 JU1934 BAM / BAI JU1934.20170531.tsv
78 JU2001 JU2001 JU2001 BAM / BAI JU2001.20170531.tsv
79 JU2007 JU2007 JU2007 BAM / BAI JU2007.20170531.tsv
80 JU2016 JU2016 JU2016 BAM / BAI JU2016.20170531.tsv
81 JU2017 JU2017 JU2017 BAM / BAI JU2017.20170531.tsv
82 JU2106 JU2106 JU2106 BAM / BAI JU2106.20170531.tsv
83 JU2131 JU2131 JU2131 BAM / BAI JU2131.20170531.tsv
84 JU2141 JU2141 JU2141 BAM / BAI JU2141.20170531.tsv
85 JU2234 JU2234 JU2234 BAM / BAI JU2234.20170531.tsv
86 JU2250 JU2250 JU2250 BAM / BAI JU2250.20170531.tsv
87 JU2257 JU2257 JU2257 JU2287 BAM / BAI JU2257.20170531.tsv
88 JU2316 JU2316 JU2316 BAM / BAI JU2316.20170531.tsv
89 JU2464 JU2464 JU2464 JU2467 JU2468 BAM / BAI JU2464.20170531.tsv
90 JU2466 JU2466 JU2466 BAM / BAI JU2466.20170531.tsv
91 JU2478 JU2478 JU2478 BAM / BAI JU2478.20170531.tsv
92 JU2513 JU2513 JU2513 BAM / BAI JU2513.20170531.tsv
93 JU2519 JU2519 JU2519 BAM / BAI JU2519.20170531.tsv
94 JU2522 JU2522 JU2522 BAM / BAI JU2522.20170531.tsv
95 JU2526 JU2526 JU2526 BAM / BAI JU2526.20170531.tsv
96 JU2534 JU2534 JU2534 BAM / BAI JU2534.20170531.tsv
97 JU2565 JU2565 JU2565 BAM / BAI JU2565.20170531.tsv
98 JU2566 JU2566 JU2566 BAM / BAI JU2566.20170531.tsv
99 JU2570 JU2570 JU2570 BAM / BAI JU2570.20170531.tsv
100 JU2572 JU2572 JU2572 BAM / BAI JU2572.20170531.tsv
101 JU2575 JU2575 JU2575 BAM / BAI JU2575.20170531.tsv
102 JU2576 JU2576 JU2576 BAM / BAI JU2576.20170531.tsv
103 JU2578 JU2578 JU2578 BAM / BAI JU2578.20170531.tsv
104 JU258 JU258 JU258 BAM / BAI JU258.20170531.tsv
105 JU2581 JU2581 JU2581 BAM / BAI JU2581.20170531.tsv
106 JU2586 JU2586 JU2586 BAM / BAI JU2586.20170531.tsv
107 JU2587 JU2587 JU2587 BAM / BAI JU2587.20170531.tsv
108 JU2592 JU2592 JU2592 BAM / BAI JU2592.20170531.tsv
109 JU2593 JU2593 JU2593 BAM / BAI JU2593.20170531.tsv
110 JU2600 JU2600 JU1924 JU2151 JU2600 JU3138 BAM / BAI JU2600.20170531.tsv
111 JU2610 JU2610 JU2610 BAM / BAI JU2610.20170531.tsv
112 JU2619 JU2619 JU2619 BAM / BAI JU2619.20170531.tsv
113 JU2800 JU2800 JU2800 JU2802 BAM / BAI JU2800.20170531.tsv
114 JU2811 JU2811 JU2811 BAM / BAI JU2811.20170531.tsv
115 JU2825 JU2825 JU2825 BAM / BAI JU2825.20170531.tsv
116 JU2829 JU2829 JU2828 JU2829 JU2830 BAM / BAI JU2829.20170531.tsv
117 JU2838 JU2838 JU2838 BAM / BAI JU2838.20170531.tsv
118 JU2841 JU2841 JU2841 BAM / BAI JU2841.20170531.tsv
119 JU2853 JU2853 JU2853 BAM / BAI JU2853.20170531.tsv
120 JU2862 JU2862 JU2862 BAM / BAI JU2862.20170531.tsv
121 JU2866 JU2866 JU2866 BAM / BAI JU2866.20170531.tsv
122 JU2878 JU2878 JU2878 BAM / BAI JU2878.20170531.tsv
123 JU2879 JU2879 JU2879 BAM / BAI JU2879.20170531.tsv
124 JU2906 JU2906 JU2906 BAM / BAI JU2906.20170531.tsv
125 JU2907 JU2907 JU2907 JU2908 BAM / BAI JU2907.20170531.tsv
126 JU310 JU310 JU1026 JU1037 JU1039 JU1040 JU1204 JU1206 JU262 JU263 JU299 JU300 JU301 JU302 JU303 JU305 JU306 JU307 JU309 JU310 JU438 BAM / BAI JU310.20170531.tsv
127 JU311 JU311 ECA551 JU311 JU312 JU313 JU314 JU315 JU316 JU317 JU318 JU319 JU321 MY2481 BAM / BAI JU311.20170531.tsv
128 JU3125 JU3125 JU3125 BAM / BAI JU3125.20170531.tsv
129 JU3127 JU3127 JU3127 BAM / BAI JU3127.20170531.tsv
130 JU3128 JU3128 JU3128 BAM / BAI JU3128.20170531.tsv
131 JU3132 JU3132 JU3132 BAM / BAI JU3132.20170531.tsv
132 JU3134 JU3134 JU3134 BAM / BAI JU3134.20170531.tsv
133 JU3135 JU3135 JU3135 BAM / BAI JU3135.20170531.tsv
134 JU3137 JU3137 JU3137 BAM / BAI JU3137.20170531.tsv
135 JU3140 JU3140 JU3140 BAM / BAI JU3140.20170531.tsv
136 JU3144 JU3144 JU3144 BAM / BAI JU3144.20170531.tsv
137 JU323 JU323 JU3131 JU322 JU323 JU342 JU347 BAM / BAI JU323.20170531.tsv
138 JU346 JU346 JU345 JU346 BAM / BAI JU346.20170531.tsv
139 JU360 JU360 JU360 JU362 JU363 JU364 JU366 JU368 JU369 JU370 JU801 BAM / BAI JU360.20170531.tsv
140 JU367 JU367 JU361 JU367 JU371 JU692 JU693 JU694 BAM / BAI JU367.20170531.tsv
141 JU393 JU393 JU393 BAM / BAI JU393.20170531.tsv
142 JU394 JU394 JU394 JU399 JU400 BAM / BAI JU394.20170531.tsv
143 JU397 JU397 JU397 JU398 JU401 JU402 BAM / BAI JU397.20170531.tsv
144 JU406 JU406 JU406 JU407 BAM / BAI JU406.20170531.tsv
145 JU440 JU440 JU440 BAM / BAI JU440.20170531.tsv
146 JU561 JU561 JU561 JU563 BAM / BAI JU561.20170531.tsv
147 JU642 JU642 JU642 BAM / BAI JU642.20170531.tsv
148 JU751 JU751 JU751 BAM / BAI JU751.20170531.tsv
149 JU774 JU774 JU774 BAM / BAI JU774.20170531.tsv
150 JU775 JU775 JU775 JU799 BAM / BAI JU775.20170531.tsv
151 JU778 JU778 JU778 BAM / BAI JU778.20170531.tsv
152 JU782 JU782 JU782 BAM / BAI JU782.20170531.tsv
153 JU792 JU792 JU2460 JU2527 JU3142 JU395 JU396 JU622 JU792 BAM / BAI JU792.20170531.tsv
154 JU830 JU830 JU829 JU830 BAM / BAI JU830.20170531.tsv
155 JU847 JU847 JU847 JU848 BAM / BAI JU847.20170531.tsv
156 KR314 KR314 KR314 BAM / BAI KR314.20170531.tsv
157 LKC34 LKC34 LKC34 BAM / BAI LKC34.20170531.tsv
158 MY1 MY1 MY1 BAM / BAI MY1.20170531.tsv
159 MY10 MY10 MY17 MY10 MY11 MY12 MY13 MY19 MY20 MY21 MY22 MY3 MY4 MY5 MY7 MY8 MY9 BAM / BAI MY10.20170531.tsv
160 MY16 MY16 MY16 BAM / BAI MY16.20170531.tsv
161 MY18 MY18 MY18 MY6 BAM / BAI MY18.20170531.tsv
162 MY2147 MY2147 MY2143 MY2147 BAM / BAI MY2147.20170531.tsv
163 MY2212 MY2212 MY2212 BAM / BAI MY2212.20170531.tsv
164 MY23 MY23 BRC20231 JU1171 MY14 MY15 MY2 MY23 BAM / BAI MY23.20170531.tsv
165 MY2453 MY2453 JU3136 MY2004 MY2011 MY2014 MY2050 MY2051 MY2054 MY2121 MY2137 MY2199 MY2288 MY2339 MY2453 MY2502 MY2541 MY2579 MY524 MY561 MY564 MY570 MY713 MY792 MY819 MY864 MY965 BAM / BAI MY2453.20170531.tsv
166 MY2530 MY2530 MY2530 BAM / BAI MY2530.20170531.tsv
167 MY2535 MY2535 MY2344 MY2532 MY2535 MY881 NIC508 NIC512 BAM / BAI MY2535.20170531.tsv
168 MY2573 MY2573 MY2142 MY2144 MY2198 MY2208 MY2224 MY2282 MY2294 MY2338 MY2434 MY2443 MY2491 MY2573 MY559 MY579 MY710 MY934 BAM / BAI MY2573.20170531.tsv
169 MY2585 MY2585 MY2585 MY2623 BAM / BAI MY2585.20170531.tsv
170 MY2693 MY2693 MY2685 MY2693 MY2719 BAM / BAI MY2693.20170531.tsv
171 MY2713 MY2713 MY2635 MY2679 MY2689 MY2713 MY803 BAM / BAI MY2713.20170531.tsv
172 MY2741 MY2741 MY2109 MY2692 MY2741 BAM / BAI MY2741.20170531.tsv
173 MY518 MY518 MY518 BAM / BAI MY518.20170531.tsv
174 MY679 MY679 MY679 MY991 BAM / BAI MY679.20170531.tsv
175 MY772 MY772 MY772 BAM / BAI MY772.20170531.tsv
176 MY795 MY795 MY2099 MY538 MY795 BAM / BAI MY795.20170531.tsv
177 MY920 MY920 MY2042 MY2138 MY2347 MY2373 MY2406 MY2688 MY589 MY741 MY887 MY920 MY990 BAM / BAI MY920.20170531.tsv
178 N2 N2 ECA253 ECA254 ECA255 ECA257 N2 BAM / BAI N2.20170531.tsv
179 NIC1 NIC1 NIC1 BAM / BAI NIC1.20170531.tsv
180 NIC1049 NIC1049 NIC1049 BAM / BAI NIC1049.20170531.tsv
181 NIC1107 NIC1107 NIC1107 BAM / BAI NIC1107.20170531.tsv
182 NIC166 NIC166 NIC166 BAM / BAI NIC166.20170531.tsv
183 NIC195 NIC195 NIC195 NIC196 NIC197 NIC198 BAM / BAI NIC195.20170531.tsv
184 NIC199 NIC199 NIC199 NIC200 BAM / BAI NIC199.20170531.tsv
185 NIC2 NIC2 NIC2 BAM / BAI NIC2.20170531.tsv
186 NIC207 NIC207 NIC207 BAM / BAI NIC207.20170531.tsv
187 NIC231 NIC231 NIC231 NIC232 BAM / BAI NIC231.20170531.tsv
188 NIC236 NIC236 NIC236 NIC237 BAM / BAI NIC236.20170531.tsv
189 NIC242 NIC242 NIC242 BAM / BAI NIC242.20170531.tsv
190 NIC251 NIC251 NIC251 BAM / BAI NIC251.20170531.tsv
191 NIC252 NIC252 NIC252 BAM / BAI NIC252.20170531.tsv
192 NIC255 NIC255 NIC255 BAM / BAI NIC255.20170531.tsv
193 NIC256 NIC256 NIC256 NIC263 BAM / BAI NIC256.20170531.tsv
194 NIC258 NIC258 NIC258 BAM / BAI NIC258.20170531.tsv
195 NIC259 NIC259 NIC259 BAM / BAI NIC259.20170531.tsv
196 NIC260 NIC260 NIC260 BAM / BAI NIC260.20170531.tsv
197 NIC261 NIC261 NIC261 BAM / BAI NIC261.20170531.tsv
198 NIC262 NIC262 NIC262 BAM / BAI NIC262.20170531.tsv
199 NIC265 NIC265 NIC265 BAM / BAI NIC265.20170531.tsv
200 NIC266 NIC266 NIC266 BAM / BAI NIC266.20170531.tsv
201 NIC267 NIC267 NIC267 NIC270 BAM / BAI NIC267.20170531.tsv
202 NIC268 NIC268 NIC268 BAM / BAI NIC268.20170531.tsv
203 NIC269 NIC269 NIC269 BAM / BAI NIC269.20170531.tsv
204 NIC271 NIC271 NIC271 BAM / BAI NIC271.20170531.tsv
205 NIC272 NIC272 NIC272 NIC273 BAM / BAI NIC272.20170531.tsv
206 NIC274 NIC274 NIC274 BAM / BAI NIC274.20170531.tsv
207 NIC275 NIC275 NIC275 BAM / BAI NIC275.20170531.tsv
208 NIC276 NIC276 NIC276 BAM / BAI NIC276.20170531.tsv
209 NIC277 NIC277 NIC277 BAM / BAI NIC277.20170531.tsv
210 NIC3 NIC3 NIC3 NIC4 BAM / BAI NIC3.20170531.tsv
211 NIC501 NIC501 NIC501 BAM / BAI NIC501.20170531.tsv
212 NIC511 NIC511 NIC511 BAM / BAI NIC511.20170531.tsv
213 NIC513 NIC513 NIC513 BAM / BAI NIC513.20170531.tsv
214 NIC514 NIC514 NIC514 BAM / BAI NIC514.20170531.tsv
215 NIC515 NIC515 NIC515 BAM / BAI NIC515.20170531.tsv
216 NIC522 NIC522 NIC522 BAM / BAI NIC522.20170531.tsv
217 NIC523 NIC523 NIC523 BAM / BAI NIC523.20170531.tsv
218 NIC526 NIC526 NIC526 BAM / BAI NIC526.20170531.tsv
219 NIC527 NIC527 NIC521 NIC527 BAM / BAI NIC527.20170531.tsv
220 NIC528 NIC528 NIC528 BAM / BAI NIC528.20170531.tsv
221 NIC529 NIC529 NIC529 BAM / BAI NIC529.20170531.tsv
222 PB303 PB303 PB303 BAM / BAI PB303.20170531.tsv
223 ECA259 PB306 ECA258 ECA259 BAM / BAI PB306.20170531.tsv
224 PS2025 PS2025 PS2025 BAM / BAI PS2025.20170531.tsv
225 PX179 PX179 PX178 PX179 BAM / BAI PX179.20170531.tsv
226 QG2075 QG2075 QG2075 BAM / BAI QG2075.20170531.tsv
227 QG536 QG536 QG536 QG537 QG538 BAM / BAI QG536.20170531.tsv
228 QG556 QG556 QG556 QG558 BAM / BAI QG556.20170531.tsv
229 QG557 QG557 QG557 BAM / BAI QG557.20170531.tsv
230 QW947 QW947 QW947 BAM / BAI QW947.20170531.tsv
231 QX1211 QX1211 QX1211 QX1215 QX1216 BAM / BAI QX1211.20170531.tsv
232 QX1212 QX1212 QX1212 QX1213 QX1214 BAM / BAI QX1212.20170531.tsv
233 QX1233 QX1233 QX1218 QX1233 BAM / BAI QX1233.20170531.tsv
234 QX1791 QX1791 QX1791 BAM / BAI QX1791.20170531.tsv
235 QX1792 QX1792 QX1792 BAM / BAI QX1792.20170531.tsv
236 QX1793 QX1793 QX1793 BAM / BAI QX1793.20170531.tsv
237 QX1794 QX1794 QX1794 BAM / BAI QX1794.20170531.tsv
238 RC301 RC301 MY2022 MY2024 MY2078 MY2291 MY2630 MY2636 MY2640 MY2681 MY2684 MY2691 MY684 MY882 RC301 BAM / BAI RC301.20170531.tsv
239 WN2001 WN2001 WN2001 WN2010 WN2011 WN2013 WN2014 WN2016 WN2017 WN2018 WN2019 WN2020 WN2021 BAM / BAI WN2001.20170531.tsv
240 WN2002 WN2002 WN2002 WN2003 BAM / BAI WN2002.20170531.tsv
241 WN2033 WN2033 WN2033 WN2035 WN2039 BAM / BAI WN2033.20170531.tsv
242 WN2050 WN2050 WN2050 WN2056 BAM / BAI WN2050.20170531.tsv
243 XZ1513 XZ1513 XZ1513 BAM / BAI XZ1513.20170531.tsv
244 XZ1514 XZ1514 XZ1514 BAM / BAI XZ1514.20170531.tsv
245 XZ1515 XZ1515 XZ1515 BAM / BAI XZ1515.20170531.tsv
246 XZ1516 XZ1516 XZ1516 BAM / BAI XZ1516.20170531.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 249 249
SNVs 2,434,802 1,865,541
Ts 1,361,672 1,041,676
Tv 1,153,388 823,865
Ts/Tv 1.18 1.26
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.

Haplotypes

Click the above image to download the full version