Releases 20170531

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Release Summary
  • Strains: 550
  • WGS strains: 410
  • Isotypes: 246
  • Genome Version WS258

Alignment Data

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

Learn about alignment data

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.

Learn more about VCF 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 anaysis 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.gz
2 BRC20067 BRC20067 BRC20067 BRC20113 BAM / bai BRC20067.20170531.tsv.gz
3 BRC20263 BRC20263 BRC20263 BAM / bai BRC20263.20170531.tsv.gz
4 ECA243 CB4851 DR1344 ECA243 RW7000 BAM / bai CB4851.20170531.tsv.gz
5 CB4852 CB4852 CB4852 JU1563 BAM / bai CB4852.20170531.tsv.gz
6 ECA246 CB4853 CB3198 DR1350 ECA245 ECA246 BAM / bai CB4853.20170531.tsv.gz
7 CB4854 CB4854 CB3196 CB3197 CB4854 BAM / bai CB4854.20170531.tsv.gz
8 ECA248 CB4855 ECA248 BAM / bai CB4855.20170531.tsv.gz
9 CB4856 CB4856 CB4856 ECA260 BAM / bai CB4856.20170531.tsv.gz
10 ECA250 CB4857 CB3199 DR1345 ECA249 ECA250 BAM / bai CB4857.20170531.tsv.gz
11 ECA251 CB4858 AB2 AB3 AB4 CX11258 CX11278 CX11305 CX11317 ECA247 ECA251 JU1960 BAM / bai CB4858.20170531.tsv.gz
12 CB4932 CB4932 CB4932 BAM / bai CB4932.20170531.tsv.gz
13 CX11254 CX11254 CX11254 BAM / bai CX11254.20170531.tsv.gz
14 CX11262 CX11262 CX11262 CX11294 BAM / bai CX11262.20170531.tsv.gz
15 CX11264 CX11264 CX11264 BAM / bai CX11264.20170531.tsv.gz
16 CX11271 CX11271 CX11271 CX11319 BAM / bai CX11271.20170531.tsv.gz
17 CX11276 CX11276 CX11276 CX11316 BAM / bai CX11276.20170531.tsv.gz
18 CX11285 CX11285 CX11285 CX11321 BAM / bai CX11285.20170531.tsv.gz
19 CX11292 CX11292 CX11259 CX11292 BAM / bai CX11292.20170531.tsv.gz
20 CX11307 CX11307 CX11307 BAM / bai CX11307.20170531.tsv.gz
21 CX11314 CX11314 CX11314 BAM / bai CX11314.20170531.tsv.gz
22 CX11315 CX11315 CX11268 CX11315 BAM / bai CX11315.20170531.tsv.gz
23 DL200 DL200 DL200 BAM / bai DL200.20170531.tsv.gz
24 DL226 DL226 DL226 BAM / bai DL226.20170531.tsv.gz
25 DL238 DL238 DL238 BAM / bai DL238.20170531.tsv.gz
26 ECA189 ECA189 ECA189 ECA190 ECA192 ECA193 ECA393 ECA395 BAM / bai ECA189.20170531.tsv.gz
27 ECA191 ECA191 ECA191 BAM / bai ECA191.20170531.tsv.gz
28 ECA348 ECA348 ECA348 BAM / bai ECA348.20170531.tsv.gz
29 ECA349 ECA349 ECA349 ECA350 BAM / bai ECA349.20170531.tsv.gz
30 ECA36 ECA36 ECA36 BAM / bai ECA36.20170531.tsv.gz
31 ECA363 ECA363 ECA363 BAM / bai ECA363.20170531.tsv.gz
32 ECA369 ECA369 ECA369 BAM / bai ECA369.20170531.tsv.gz
33 ECA372 ECA372 ECA372 BAM / bai ECA372.20170531.tsv.gz
34 ECA396 ECA396 ECA396 ECA397 ECA398 ECA399 BAM / bai ECA396.20170531.tsv.gz
35 ED3005 ED3005 ED3005 ED3021 BAM / bai ED3005.20170531.tsv.gz
36 ED3011 ED3011 ED3011 BAM / bai ED3011.20170531.tsv.gz
37 ED3012 ED3012 ED3010 ED3012 ED3014 ED3015 ED3023 ED3024 ED3028 BAM / bai ED3012.20170531.tsv.gz
38 ED3017 ED3017 ED3017 ED3019 ED3020 BAM / bai ED3017.20170531.tsv.gz
39 ED3040 ED3040 ED3040 BAM / bai ED3040.20170531.tsv.gz
40 ED3046 ED3046 ED3046 BAM / bai ED3046.20170531.tsv.gz
41 ED3048 ED3048 ED3042 ED3048 BAM / bai ED3048.20170531.tsv.gz
42 ED3049 ED3049 ED3049 BAM / bai ED3049.20170531.tsv.gz
43 ED3052 ED3052 ED3043 ED3052 BAM / bai ED3052.20170531.tsv.gz
44 ED3073 ED3073 ED3057 ED3072 ED3073 ED3075 BAM / bai ED3073.20170531.tsv.gz
45 ED3077 ED3077 ED3077 BAM / bai ED3077.20170531.tsv.gz
46 EG4347 EG4347 EG4346 EG4347 BAM / bai EG4347.20170531.tsv.gz
47 EG4349 EG4349 EG4348 EG4349 BAM / bai EG4349.20170531.tsv.gz
48 EG4724 EG4724 EG4724 BAM / bai EG4724.20170531.tsv.gz
49 EG4725 EG4725 EG4725 BAM / bai EG4725.20170531.tsv.gz
50 EG4946 EG4946 EG4680 EG4689 EG4945 EG4946 EG4948 EG4951 EG4957 BAM / bai EG4946.20170531.tsv.gz
51 GXW1 GXW1 GXW1 BAM / bai GXW1.20170531.tsv.gz
52 JT11398 JT11398 JT11362 JT11398 JT11399 BAM / bai JT11398.20170531.tsv.gz
53 JU1088 JU1088 JU1088 BAM / bai JU1088.20170531.tsv.gz
54 JU1172 JU1172 JU1172 BAM / bai JU1172.20170531.tsv.gz
55 JU1200 JU1200 JU1200 JU2860 BAM / bai JU1200.20170531.tsv.gz
56 JU1212 JU1212 JU1207 JU1212 JU1214 BAM / bai JU1212.20170531.tsv.gz
57 JU1213 JU1213 JU1213 JU1482 JU531 JU533 JU1656 JU1762 JU1770 BAM / bai JU1213.20170531.tsv.gz
58 JU1242 JU1242 JU1218 JU1230 JU1242 JU1243 BAM / bai JU1242.20170531.tsv.gz
59 JU1246 JU1246 JU1246 BAM / bai JU1246.20170531.tsv.gz
60 JU1249 JU1249 JU1249 BAM / bai JU1249.20170531.tsv.gz
61 JU1395 JU1395 ECA589 JU1395 BAM / bai JU1395.20170531.tsv.gz
62 JU1400 JU1400 JU1400 BAM / bai JU1400.20170531.tsv.gz
63 JU1409 JU1409 JU1401 JU1409 JU1410 JU1411 BAM / bai JU1409.20170531.tsv.gz
64 JU1440 JU1440 JU1440 JU3133 BAM / bai JU1440.20170531.tsv.gz
65 JU1491 JU1491 JU1484 JU1491 BAM / bai JU1491.20170531.tsv.gz
66 JU1530 JU1530 ECA616 JU1530 BAM / bai JU1530.20170531.tsv.gz
67 JU1543 JU1543 JU1543 BAM / bai JU1543.20170531.tsv.gz
68 JU1568 JU1568 JU1566 JU1568 BAM / bai JU1568.20170531.tsv.gz
69 JU1581 JU1581 JU1516 JU1522 JU1581 JU1582 ECA615 JU1807 BAM / bai JU1581.20170531.tsv.gz
70 JU1586 JU1586 JU1586 BAM / bai JU1586.20170531.tsv.gz
71 JU1652 JU1652 JU1652 BAM / bai JU1652.20170531.tsv.gz
72 JU1666 JU1666 JU1666 JU3139 BAM / bai JU1666.20170531.tsv.gz
73 JU1792 JU1792 JU1792 BAM / bai JU1792.20170531.tsv.gz
74 JU1793 JU1793 JU1793 JU1920 JU1922 JU1929 JU2139 JU2604 JU2605 BAM / bai JU1793.20170531.tsv.gz
75 JU1808 JU1808 JU1808 BAM / bai JU1808.20170531.tsv.gz
76 JU1896 JU1896 JU1896 BAM / bai JU1896.20170531.tsv.gz
77 JU1934 JU1934 JU1934 BAM / bai JU1934.20170531.tsv.gz
78 JU2001 JU2001 JU2001 BAM / bai JU2001.20170531.tsv.gz
79 JU2007 JU2007 JU2007 BAM / bai JU2007.20170531.tsv.gz
80 JU2016 JU2016 JU2016 BAM / bai JU2016.20170531.tsv.gz
81 JU2017 JU2017 JU2017 BAM / bai JU2017.20170531.tsv.gz
82 JU2106 JU2106 JU2106 BAM / bai JU2106.20170531.tsv.gz
83 JU2131 JU2131 JU2131 BAM / bai JU2131.20170531.tsv.gz
84 JU2141 JU2141 JU2141 BAM / bai JU2141.20170531.tsv.gz
85 JU2234 JU2234 JU2234 BAM / bai JU2234.20170531.tsv.gz
86 JU2250 JU2250 JU2250 BAM / bai JU2250.20170531.tsv.gz
87 JU2257 JU2257 JU2257 JU2287 BAM / bai JU2257.20170531.tsv.gz
88 JU2316 JU2316 JU2316 BAM / bai JU2316.20170531.tsv.gz
89 JU2464 JU2464 JU2464 JU2467 JU2468 BAM / bai JU2464.20170531.tsv.gz
90 JU2466 JU2466 JU2466 BAM / bai JU2466.20170531.tsv.gz
91 JU2478 JU2478 JU2478 BAM / bai JU2478.20170531.tsv.gz
92 JU2513 JU2513 JU2513 BAM / bai JU2513.20170531.tsv.gz
93 JU2519 JU2519 JU2519 BAM / bai JU2519.20170531.tsv.gz
94 JU2522 JU2522 JU2522 BAM / bai JU2522.20170531.tsv.gz
95 JU2526 JU2526 JU2526 BAM / bai JU2526.20170531.tsv.gz
96 JU2534 JU2534 JU2534 BAM / bai JU2534.20170531.tsv.gz
97 JU2565 JU2565 JU2565 BAM / bai JU2565.20170531.tsv.gz
98 JU2566 JU2566 JU2566 BAM / bai JU2566.20170531.tsv.gz
99 JU2570 JU2570 JU2570 BAM / bai JU2570.20170531.tsv.gz
100 JU2572 JU2572 JU2572 BAM / bai JU2572.20170531.tsv.gz
101 JU2575 JU2575 JU2575 BAM / bai JU2575.20170531.tsv.gz
102 JU2576 JU2576 JU2576 BAM / bai JU2576.20170531.tsv.gz
103 JU2578 JU2578 JU2578 BAM / bai JU2578.20170531.tsv.gz
104 JU258 JU258 JU258 BAM / bai JU258.20170531.tsv.gz
105 JU2581 JU2581 JU2581 BAM / bai JU2581.20170531.tsv.gz
106 JU2586 JU2586 JU2586 BAM / bai JU2586.20170531.tsv.gz
107 JU2587 JU2587 JU2587 BAM / bai JU2587.20170531.tsv.gz
108 JU2592 JU2592 JU2592 BAM / bai JU2592.20170531.tsv.gz
109 JU2593 JU2593 JU2593 BAM / bai JU2593.20170531.tsv.gz
110 JU2600 JU2600 JU1924 JU2151 JU2600 JU3138 BAM / bai JU2600.20170531.tsv.gz
111 JU2610 JU2610 JU2610 BAM / bai JU2610.20170531.tsv.gz
112 JU2619 JU2619 JU2619 BAM / bai JU2619.20170531.tsv.gz
113 JU2800 JU2800 JU2800 JU2802 BAM / bai JU2800.20170531.tsv.gz
114 JU2811 JU2811 JU2811 BAM / bai JU2811.20170531.tsv.gz
115 JU2825 JU2825 JU2825 BAM / bai JU2825.20170531.tsv.gz
116 JU2829 JU2829 JU2828 JU2829 JU2830 BAM / bai JU2829.20170531.tsv.gz
117 JU2838 JU2838 JU2838 BAM / bai JU2838.20170531.tsv.gz
118 JU2841 JU2841 JU2841 BAM / bai JU2841.20170531.tsv.gz
119 JU2853 JU2853 JU2853 BAM / bai JU2853.20170531.tsv.gz
120 JU2862 JU2862 JU2862 BAM / bai JU2862.20170531.tsv.gz
121 JU2866 JU2866 JU2866 BAM / bai JU2866.20170531.tsv.gz
122 JU2878 JU2878 JU2878 BAM / bai JU2878.20170531.tsv.gz
123 JU2879 JU2879 JU2879 BAM / bai JU2879.20170531.tsv.gz
124 JU2906 JU2906 JU2906 BAM / bai JU2906.20170531.tsv.gz
125 JU2907 JU2907 JU2907 JU2908 BAM / bai JU2907.20170531.tsv.gz
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.gz
127 JU311 JU311 JU311 JU312 JU313 JU314 JU315 JU316 JU317 JU318 JU319 JU321 ECA551 MY2481 BAM / bai JU311.20170531.tsv.gz
128 JU3125 JU3125 JU3125 BAM / bai JU3125.20170531.tsv.gz
129 JU3127 JU3127 JU3127 BAM / bai JU3127.20170531.tsv.gz
130 JU3128 JU3128 JU3128 BAM / bai JU3128.20170531.tsv.gz
131 JU3132 JU3132 JU3132 BAM / bai JU3132.20170531.tsv.gz
132 JU3134 JU3134 JU3134 BAM / bai JU3134.20170531.tsv.gz
133 JU3135 JU3135 JU3135 BAM / bai JU3135.20170531.tsv.gz
134 JU3137 JU3137 JU3137 BAM / bai JU3137.20170531.tsv.gz
135 JU3140 JU3140 JU3140 BAM / bai JU3140.20170531.tsv.gz
136 JU3144 JU3144 JU3144 BAM / bai JU3144.20170531.tsv.gz
137 JU323 JU323 JU322 JU323 JU342 JU347 JU3131 BAM / bai JU323.20170531.tsv.gz
138 JU346 JU346 JU346 JU345 BAM / bai JU346.20170531.tsv.gz
139 JU360 JU360 JU360 JU362 JU363 JU364 JU366 JU368 JU369 JU370 JU801 BAM / bai JU360.20170531.tsv.gz
140 JU367 JU367 JU361 JU367 JU371 JU692 JU693 JU694 BAM / bai JU367.20170531.tsv.gz
141 JU393 JU393 JU393 BAM / bai JU393.20170531.tsv.gz
142 JU394 JU394 JU394 JU399 JU400 BAM / bai JU394.20170531.tsv.gz
143 JU397 JU397 JU397 JU398 JU401 JU402 BAM / bai JU397.20170531.tsv.gz
144 JU406 JU406 JU406 JU407 BAM / bai JU406.20170531.tsv.gz
145 JU440 JU440 JU440 BAM / bai JU440.20170531.tsv.gz
146 JU561 JU561 JU561 JU563 BAM / bai JU561.20170531.tsv.gz
147 JU642 JU642 JU642 BAM / bai JU642.20170531.tsv.gz
148 JU751 JU751 JU751 BAM / bai JU751.20170531.tsv.gz
149 JU774 JU774 JU774 BAM / bai JU774.20170531.tsv.gz
150 JU775 JU775 JU775 JU799 BAM / bai JU775.20170531.tsv.gz
151 JU778 JU778 JU778 BAM / bai JU778.20170531.tsv.gz
152 JU782 JU782 JU782 BAM / bai JU782.20170531.tsv.gz
153 JU792 JU792 JU395 JU396 JU622 JU792 JU2460 JU2527 JU3142 BAM / bai JU792.20170531.tsv.gz
154 JU830 JU830 JU829 JU830 BAM / bai JU830.20170531.tsv.gz
155 JU847 JU847 JU847 JU848 BAM / bai JU847.20170531.tsv.gz
156 KR314 KR314 KR314 BAM / bai KR314.20170531.tsv.gz
157 LKC34 LKC34 LKC34 BAM / bai LKC34.20170531.tsv.gz
158 MY1 MY1 MY1 BAM / bai MY1.20170531.tsv.gz
159 MY10 MY10 MY10 MY11 MY12 MY13 MY17 MY19 MY20 MY21 MY22 MY3 MY4 MY5 MY7 MY8 MY9 BAM / bai MY10.20170531.tsv.gz
160 MY16 MY16 MY16 BAM / bai MY16.20170531.tsv.gz
161 MY18 MY18 MY18 MY6 BAM / bai MY18.20170531.tsv.gz
162 MY2147 MY2147 MY2143 MY2147 BAM / bai MY2147.20170531.tsv.gz
163 MY2212 MY2212 MY2212 BAM / bai MY2212.20170531.tsv.gz
164 MY23 MY23 JU1171 MY14 MY15 MY2 MY23 BRC20231 BAM / bai MY23.20170531.tsv.gz
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.gz
166 MY2530 MY2530 MY2530 BAM / bai MY2530.20170531.tsv.gz
167 MY2535 MY2535 MY2344 MY2532 MY2535 MY881 NIC508 NIC512 BAM / bai MY2535.20170531.tsv.gz
168 MY2573 MY2573 MY2142 MY2144 MY2198 MY2208 MY2224 MY2282 MY2294 MY2338 MY2434 MY2443 MY2491 MY2573 MY559 MY579 MY710 MY934 BAM / bai MY2573.20170531.tsv.gz
169 MY2585 MY2585 MY2585 MY2623 BAM / bai MY2585.20170531.tsv.gz
170 MY2693 MY2693 MY2685 MY2693 MY2719 BAM / bai MY2693.20170531.tsv.gz
171 MY2713 MY2713 MY2635 MY2679 MY2689 MY2713 MY803 BAM / bai MY2713.20170531.tsv.gz
172 MY2741 MY2741 MY2109 MY2692 MY2741 BAM / bai MY2741.20170531.tsv.gz
173 MY518 MY518 MY518 BAM / bai MY518.20170531.tsv.gz
174 MY679 MY679 MY679 MY991 BAM / bai MY679.20170531.tsv.gz
175 MY772 MY772 MY772 BAM / bai MY772.20170531.tsv.gz
176 MY795 MY795 MY2099 MY538 MY795 BAM / bai MY795.20170531.tsv.gz
177 MY920 MY920 MY2042 MY2138 MY2347 MY2373 MY2406 MY2688 MY589 MY741 MY887 MY920 MY990 BAM / bai MY920.20170531.tsv.gz
178 N2 N2 ECA253 ECA254 ECA255 ECA257 N2 BAM / bai N2.20170531.tsv.gz
179 NIC1 NIC1 NIC1 BAM / bai NIC1.20170531.tsv.gz
180 NIC1049 NIC1049 NIC1049 BAM / bai NIC1049.20170531.tsv.gz
181 NIC1107 NIC1107 NIC1107 BAM / bai NIC1107.20170531.tsv.gz
182 NIC166 NIC166 NIC166 BAM / bai NIC166.20170531.tsv.gz
183 NIC195 NIC195 NIC195 NIC196 NIC197 NIC198 BAM / bai NIC195.20170531.tsv.gz
184 NIC199 NIC199 NIC199 NIC200 BAM / bai NIC199.20170531.tsv.gz
185 NIC2 NIC2 NIC2 BAM / bai NIC2.20170531.tsv.gz
186 NIC207 NIC207 NIC207 BAM / bai NIC207.20170531.tsv.gz
187 NIC231 NIC231 NIC231 NIC232 BAM / bai NIC231.20170531.tsv.gz
188 NIC236 NIC236 NIC236 NIC237 BAM / bai NIC236.20170531.tsv.gz
189 NIC242 NIC242 NIC242 BAM / bai NIC242.20170531.tsv.gz
190 NIC251 NIC251 NIC251 BAM / bai NIC251.20170531.tsv.gz
191 NIC252 NIC252 NIC252 BAM / bai NIC252.20170531.tsv.gz
192 NIC255 NIC255 NIC255 BAM / bai NIC255.20170531.tsv.gz
193 NIC256 NIC256 NIC256 NIC263 BAM / bai NIC256.20170531.tsv.gz
194 NIC258 NIC258 NIC258 BAM / bai NIC258.20170531.tsv.gz
195 NIC259 NIC259 NIC259 BAM / bai NIC259.20170531.tsv.gz
196 NIC260 NIC260 NIC260 BAM / bai NIC260.20170531.tsv.gz
197 NIC261 NIC261 NIC261 BAM / bai NIC261.20170531.tsv.gz
198 NIC262 NIC262 NIC262 BAM / bai NIC262.20170531.tsv.gz
199 NIC265 NIC265 NIC265 BAM / bai NIC265.20170531.tsv.gz
200 NIC266 NIC266 NIC266 BAM / bai NIC266.20170531.tsv.gz
201 NIC267 NIC267 NIC267 NIC270 BAM / bai NIC267.20170531.tsv.gz
202 NIC268 NIC268 NIC268 BAM / bai NIC268.20170531.tsv.gz
203 NIC269 NIC269 NIC269 BAM / bai NIC269.20170531.tsv.gz
204 NIC271 NIC271 NIC271 BAM / bai NIC271.20170531.tsv.gz
205 NIC272 NIC272 NIC272 NIC273 BAM / bai NIC272.20170531.tsv.gz
206 NIC274 NIC274 NIC274 BAM / bai NIC274.20170531.tsv.gz
207 NIC275 NIC275 NIC275 BAM / bai NIC275.20170531.tsv.gz
208 NIC276 NIC276 NIC276 BAM / bai NIC276.20170531.tsv.gz
209 NIC277 NIC277 NIC277 BAM / bai NIC277.20170531.tsv.gz
210 NIC3 NIC3 NIC3 NIC4 BAM / bai NIC3.20170531.tsv.gz
211 NIC501 NIC501 NIC501 BAM / bai NIC501.20170531.tsv.gz
212 NIC511 NIC511 NIC511 BAM / bai NIC511.20170531.tsv.gz
213 NIC513 NIC513 NIC513 BAM / bai NIC513.20170531.tsv.gz
214 NIC514 NIC514 NIC514 BAM / bai NIC514.20170531.tsv.gz
215 NIC515 NIC515 NIC515 BAM / bai NIC515.20170531.tsv.gz
216 NIC522 NIC522 NIC522 BAM / bai NIC522.20170531.tsv.gz
217 NIC523 NIC523 NIC523 BAM / bai NIC523.20170531.tsv.gz
218 NIC526 NIC526 NIC526 BAM / bai NIC526.20170531.tsv.gz
219 NIC527 NIC527 NIC521 NIC527 BAM / bai NIC527.20170531.tsv.gz
220 NIC528 NIC528 NIC528 BAM / bai NIC528.20170531.tsv.gz
221 NIC529 NIC529 NIC529 BAM / bai NIC529.20170531.tsv.gz
222 PB303 PB303 PB303 BAM / bai PB303.20170531.tsv.gz
223 ECA259 PB306 ECA258 ECA259 BAM / bai PB306.20170531.tsv.gz
224 PS2025 PS2025 PS2025 BAM / bai PS2025.20170531.tsv.gz
225 PX179 PX179 PX178 PX179 BAM / bai PX179.20170531.tsv.gz
226 QG2075 QG2075 QG2075 BAM / bai QG2075.20170531.tsv.gz
227 QG536 QG536 QG536 QG537 QG538 BAM / bai QG536.20170531.tsv.gz
228 QG556 QG556 QG556 QG558 BAM / bai QG556.20170531.tsv.gz
229 QG557 QG557 QG557 BAM / bai QG557.20170531.tsv.gz
230 QW947 QW947 QW947 BAM / bai QW947.20170531.tsv.gz
231 QX1211 QX1211 QX1211 QX1215 QX1216 BAM / bai QX1211.20170531.tsv.gz
232 QX1212 QX1212 QX1212 QX1213 QX1214 BAM / bai QX1212.20170531.tsv.gz
233 QX1233 QX1233 QX1218 QX1233 BAM / bai QX1233.20170531.tsv.gz
234 QX1791 QX1791 QX1791 BAM / bai QX1791.20170531.tsv.gz
235 QX1792 QX1792 QX1792 BAM / bai QX1792.20170531.tsv.gz
236 QX1793 QX1793 QX1793 BAM / bai QX1793.20170531.tsv.gz
237 QX1794 QX1794 QX1794 BAM / bai QX1794.20170531.tsv.gz
238 RC301 RC301 RC301 MY2022 MY2024 MY2078 MY2291 MY2630 MY2636 MY2640 MY2681 MY2684 MY2691 MY684 MY882 BAM / bai RC301.20170531.tsv.gz
239 WN2001 WN2001 WN2001 WN2010 WN2011 WN2013 WN2014 WN2016 WN2017 WN2018 WN2019 WN2020 WN2021 BAM / bai WN2001.20170531.tsv.gz
240 WN2002 WN2002 WN2002 WN2003 BAM / bai WN2002.20170531.tsv.gz
241 WN2033 WN2033 WN2033 WN2035 WN2039 BAM / bai WN2033.20170531.tsv.gz
242 WN2050 WN2050 WN2050 WN2056 BAM / bai WN2050.20170531.tsv.gz
243 XZ1513 XZ1513 XZ1513 BAM / bai XZ1513.20170531.tsv.gz
244 XZ1514 XZ1514 XZ1514 BAM / bai XZ1514.20170531.tsv.gz
245 XZ1515 XZ1515 XZ1515 BAM / bai XZ1515.20170531.tsv.gz
246 XZ1516 XZ1516 XZ1516 BAM / bai XZ1516.20170531.tsv.gz


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 / Pipelines

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