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Genomic Data

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Release Summary
  • Strains: 753
  • WGS strains: 613
  • Isotypes: 330
  • Genome: WS263

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 AB1.20180527.tsv.gz
2 BRC20067 BRC20067 BRC20067 BRC20113 BAM / BAI BRC20067.20180527.tsv.gz
3 BRC20263 BRC20263 BRC20263 BAM / BAI BRC20263.20180527.tsv.gz
4 ECA243 CB4851 DR1344 ECA243 RW7000 BAM / BAI CB4851.20180527.tsv.gz
5 CB4852 CB4852 CB4852 JU1563 BAM / BAI CB4852.20180527.tsv.gz
6 ECA246 CB4853 CB3198 DR1350 ECA245 ECA246 BAM / BAI CB4853.20180527.tsv.gz
7 CB4854 CB4854 CB3196 CB3197 CB4854 BAM / BAI CB4854.20180527.tsv.gz
8 ECA248 CB4855 ECA248 BAM / BAI CB4855.20180527.tsv.gz
9 CB4856 CB4856 CB4856 ECA260 BAM / BAI CB4856.20180527.tsv.gz
10 ECA250 CB4857 CB3199 DR1345 ECA249 ECA250 BAM / BAI CB4857.20180527.tsv.gz
11 ECA251 CB4858 AB2 AB3 AB4 CX11258 CX11278 CX11305 CX11317 ECA247 ECA251 JU1960 BAM / BAI CB4858.20180527.tsv.gz
12 CB4932 CB4932 CB4932 BAM / BAI CB4932.20180527.tsv.gz
13 CX11254 CX11254 CX11254 BAM / BAI CX11254.20180527.tsv.gz
14 CX11262 CX11262 CX11262 CX11294 BAM / BAI CX11262.20180527.tsv.gz
15 CX11264 CX11264 CX11264 BAM / BAI CX11264.20180527.tsv.gz
16 CX11271 CX11271 CX11271 CX11319 BAM / BAI CX11271.20180527.tsv.gz
17 CX11276 CX11276 CX11276 CX11316 BAM / BAI CX11276.20180527.tsv.gz
18 CX11285 CX11285 CX11285 CX11321 BAM / BAI CX11285.20180527.tsv.gz
19 CX11292 CX11292 CX11259 CX11292 BAM / BAI CX11292.20180527.tsv.gz
20 CX11307 CX11307 CX11307 BAM / BAI CX11307.20180527.tsv.gz
21 CX11314 CX11314 CX11314 BAM / BAI CX11314.20180527.tsv.gz
22 CX11315 CX11315 CX11268 CX11315 BAM / BAI CX11315.20180527.tsv.gz
23 DL200 DL200 DL200 BAM / BAI DL200.20180527.tsv.gz
24 DL226 DL226 DL226 BAM / BAI DL226.20180527.tsv.gz
25 DL238 DL238 DL238 BAM / BAI DL238.20180527.tsv.gz
26 ECA189 ECA189 ECA189 ECA190 ECA192 ECA193 ECA393 ECA394 ECA395 BAM / BAI ECA189.20180527.tsv.gz
27 ECA191 ECA191 ECA191 BAM / BAI ECA191.20180527.tsv.gz
28 ECA347 ECA347 ECA347 BAM / BAI ECA347.20180527.tsv.gz
29 ECA348 ECA348 ECA348 BAM / BAI ECA348.20180527.tsv.gz
30 ECA349 ECA349 ECA349 ECA350 BAM / BAI ECA349.20180527.tsv.gz
31 ECA36 ECA36 ECA36 BAM / BAI ECA36.20180527.tsv.gz
32 ECA363 ECA363 ECA363 BAM / BAI ECA363.20180527.tsv.gz
33 ECA369 ECA369 ECA369 BAM / BAI ECA369.20180527.tsv.gz
34 ECA372 ECA372 ECA372 BAM / BAI ECA372.20180527.tsv.gz
35 ECA396 ECA396 ECA396 ECA397 ECA398 ECA399 BAM / BAI ECA396.20180527.tsv.gz
36 ECA592 ECA592 ECA592 BAM / BAI ECA592.20180527.tsv.gz
37 ECA593 ECA593 ECA593 BAM / BAI ECA593.20180527.tsv.gz
38 ECA594 ECA594 ECA594 BAM / BAI ECA594.20180527.tsv.gz
39 ECA640 ECA640 ECA640 BAM / BAI ECA640.20180527.tsv.gz
40 ECA701 ECA701 ECA701 ECA702 BAM / BAI ECA701.20180527.tsv.gz
41 ECA703 ECA703 ECA703 BAM / BAI ECA703.20180527.tsv.gz
42 ECA705 ECA705 ECA705 ECA822 BAM / BAI ECA705.20180527.tsv.gz
43 ECA706 ECA706 ECA706 BAM / BAI ECA706.20180527.tsv.gz
44 ECA710 ECA710 ECA710 BAM / BAI ECA710.20180527.tsv.gz
45 ECA712 ECA712 ECA711 ECA712 ECA713 ECA714 ECA715 BAM / BAI ECA712.20180527.tsv.gz
46 ECA722 ECA722 ECA722 BAM / BAI ECA722.20180527.tsv.gz
47 ECA723 ECA723 ECA723 ECA728 ECA729 BAM / BAI ECA723.20180527.tsv.gz
48 ECA724 ECA724 ECA724 ECA725 ECA726 ECA727 BAM / BAI ECA724.20180527.tsv.gz
49 ECA730 ECA730 ECA730 BAM / BAI ECA730.20180527.tsv.gz
50 ECA732 ECA732 ECA732 BAM / BAI ECA732.20180527.tsv.gz
51 ECA733 ECA733 ECA731 ECA733 BAM / BAI ECA733.20180527.tsv.gz
52 ECA738 ECA738 ECA734 ECA735 ECA736 ECA737 ECA738 BAM / BAI ECA738.20180527.tsv.gz
53 ECA740 ECA740 ECA740 BAM / BAI ECA740.20180527.tsv.gz
54 ECA741 ECA741 ECA741 BAM / BAI ECA741.20180527.tsv.gz
55 ECA742 ECA742 ECA742 BAM / BAI ECA742.20180527.tsv.gz
56 ECA743 ECA743 ECA743 BAM / BAI ECA743.20180527.tsv.gz
57 ECA744 ECA744 ECA744 BAM / BAI ECA744.20180527.tsv.gz
58 ECA745 ECA745 ECA745 ECA747 BAM / BAI ECA745.20180527.tsv.gz
59 ECA746 ECA746 ECA746 BAM / BAI ECA746.20180527.tsv.gz
60 ECA760 ECA760 ECA739 ECA749 ECA752 ECA753 ECA754 ECA758 ECA760 ECA769 ECA779 ECA780 ECA784 ECA785 ECA808 BAM / BAI ECA760.20180527.tsv.gz
61 ECA768 ECA768 ECA768 ECA772 BAM / BAI ECA768.20180527.tsv.gz
62 ECA777 ECA777 ECA777 BAM / BAI ECA777.20180527.tsv.gz
63 ECA778 ECA778 ECA707 ECA708 ECA709 ECA721 ECA756 ECA757 ECA763 ECA764 ECA765 ECA766 ECA767 ECA778 ECA781 ECA810 ECA811 BAM / BAI ECA778.20180527.tsv.gz
64 ECA807 ECA807 ECA716 ECA717 ECA718 ECA720 ECA770 ECA807 BAM / BAI ECA807.20180527.tsv.gz
65 ECA812 ECA812 ECA704 ECA719 ECA748 ECA750 ECA751 ECA755 ECA759 ECA761 ECA762 ECA771 ECA773 ECA774 ECA775 ECA776 ECA782 ECA783 ECA786 ECA787 ECA809 ECA812 ECA813 BAM / BAI ECA812.20180527.tsv.gz
66 ECA923 ECA923 ECA922 ECA923 ECA924 ECA925 ECA927 BAM / BAI ECA923.20180527.tsv.gz
67 ECA928 ECA928 ECA926 ECA928 BAM / BAI ECA928.20180527.tsv.gz
68 ECA930 ECA930 ECA930 BAM / BAI ECA930.20180527.tsv.gz
69 ED3005 ED3005 ED3005 ED3021 BAM / BAI ED3005.20180527.tsv.gz
70 ED3011 ED3011 ED3011 BAM / BAI ED3011.20180527.tsv.gz
71 ED3012 ED3012 ED3010 ED3012 ED3014 ED3015 ED3023 ED3024 ED3028 BAM / BAI ED3012.20180527.tsv.gz
72 ED3017 ED3017 ED3017 ED3019 ED3020 BAM / BAI ED3017.20180527.tsv.gz
73 ED3040 ED3040 ED3040 BAM / BAI ED3040.20180527.tsv.gz
74 ED3046 ED3046 ED3046 BAM / BAI ED3046.20180527.tsv.gz
75 ED3048 ED3048 ED3042 ED3048 BAM / BAI ED3048.20180527.tsv.gz
76 ED3049 ED3049 ED3049 BAM / BAI ED3049.20180527.tsv.gz
77 ED3052 ED3052 ED3043 ED3052 BAM / BAI ED3052.20180527.tsv.gz
78 ED3073 ED3073 ECA571 ECA572 ED3057 ED3072 ED3073 ED3075 BAM / BAI ED3073.20180527.tsv.gz
79 ED3077 ED3077 ED3077 BAM / BAI ED3077.20180527.tsv.gz
80 EG4347 EG4347 EG4346 EG4347 BAM / BAI EG4347.20180527.tsv.gz
81 EG4349 EG4349 EG4348 EG4349 BAM / BAI EG4349.20180527.tsv.gz
82 EG4724 EG4724 EG4724 BAM / BAI EG4724.20180527.tsv.gz
83 EG4725 EG4725 EG4725 BAM / BAI EG4725.20180527.tsv.gz
84 EG4946 EG4946 EG4680 EG4689 EG4945 EG4946 EG4948 EG4951 EG4957 BAM / BAI EG4946.20180527.tsv.gz
85 GXW1 GXW1 GXW1 BAM / BAI GXW1.20180527.tsv.gz
86 JT11398 JT11398 JT11362 JT11398 JT11399 BAM / BAI JT11398.20180527.tsv.gz
87 JU1088 JU1088 JU1088 BAM / BAI JU1088.20180527.tsv.gz
88 JU1172 JU1172 JU1172 BAM / BAI JU1172.20180527.tsv.gz
89 JU1200 JU1200 JU1200 JU2860 BAM / BAI JU1200.20180527.tsv.gz
90 JU1212 JU1212 JU1207 JU1212 JU1214 BAM / BAI JU1212.20180527.tsv.gz
91 JU1213 JU1213 JU1213 JU1482 JU1656 JU1762 JU1770 JU531 JU533 BAM / BAI JU1213.20180527.tsv.gz
92 JU1242 JU1242 JU1218 JU1230 JU1242 JU1243 BAM / BAI JU1242.20180527.tsv.gz
93 JU1246 JU1246 JU1246 BAM / BAI JU1246.20180527.tsv.gz
94 JU1249 JU1249 JU1249 BAM / BAI JU1249.20180527.tsv.gz
95 JU1395 JU1395 ECA589 JU1395 BAM / BAI JU1395.20180527.tsv.gz
96 JU1400 JU1400 JU1400 BAM / BAI JU1400.20180527.tsv.gz
97 JU1409 JU1409 JU1401 JU1409 JU1410 JU1411 BAM / BAI JU1409.20180527.tsv.gz
98 JU1440 JU1440 JU1440 JU3133 BAM / BAI JU1440.20180527.tsv.gz
99 JU1491 JU1491 JU1484 JU1491 BAM / BAI JU1491.20180527.tsv.gz
100 JU1530 JU1530 ECA616 JU1530 BAM / BAI JU1530.20180527.tsv.gz
101 JU1543 JU1543 JU1543 BAM / BAI JU1543.20180527.tsv.gz
102 JU1568 JU1568 JU1566 JU1568 BAM / BAI JU1568.20180527.tsv.gz
103 JU1581 JU1581 ECA615 JU1516 JU1522 JU1581 JU1582 JU1807 BAM / BAI JU1581.20180527.tsv.gz
104 JU1586 JU1586 JU1586 BAM / BAI JU1586.20180527.tsv.gz
105 JU1652 JU1652 JU1652 BAM / BAI JU1652.20180527.tsv.gz
106 JU1666 JU1666 JU1666 JU3139 BAM / BAI JU1666.20180527.tsv.gz
107 JU1792 JU1792 JU1792 BAM / BAI JU1792.20180527.tsv.gz
108 JU1793 JU1793 JU1793 JU1920 JU1922 JU1929 JU2139 JU2604 JU2605 JU3271 BAM / BAI JU1793.20180527.tsv.gz
109 JU1808 JU1808 JU1808 BAM / BAI JU1808.20180527.tsv.gz
110 JU1896 JU1896 JU1896 BAM / BAI JU1896.20180527.tsv.gz
111 JU1934 JU1934 JU1934 BAM / BAI JU1934.20180527.tsv.gz
112 JU2001 JU2001 JU2001 BAM / BAI JU2001.20180527.tsv.gz
113 JU2007 JU2007 JU2007 BAM / BAI JU2007.20180527.tsv.gz
114 JU2016 JU2016 JU2016 BAM / BAI JU2016.20180527.tsv.gz
115 JU2017 JU2017 JU2017 BAM / BAI JU2017.20180527.tsv.gz
116 JU2106 JU2106 JU2106 BAM / BAI JU2106.20180527.tsv.gz
117 JU2131 JU2131 JU2131 BAM / BAI JU2131.20180527.tsv.gz
118 JU2141 JU2141 JU2141 BAM / BAI JU2141.20180527.tsv.gz
119 JU2234 JU2234 JU2234 BAM / BAI JU2234.20180527.tsv.gz
120 JU2250 JU2250 JU2250 BAM / BAI JU2250.20180527.tsv.gz
121 JU2257 JU2257 JU2257 JU2287 BAM / BAI JU2257.20180527.tsv.gz
122 JU2316 JU2316 JU2316 BAM / BAI JU2316.20180527.tsv.gz
123 JU2464 JU2464 JU2464 JU2467 JU2468 BAM / BAI JU2464.20180527.tsv.gz
124 JU2466 JU2466 JU2466 BAM / BAI JU2466.20180527.tsv.gz
125 JU2478 JU2478 JU2478 BAM / BAI JU2478.20180527.tsv.gz
126 JU2513 JU2513 JU2513 BAM / BAI JU2513.20180527.tsv.gz
127 JU2519 JU2519 JU2519 BAM / BAI JU2519.20180527.tsv.gz
128 JU2522 JU2522 JU2522 BAM / BAI JU2522.20180527.tsv.gz
129 JU2526 JU2526 JU2526 BAM / BAI JU2526.20180527.tsv.gz
130 JU2534 JU2534 JU2534 BAM / BAI JU2534.20180527.tsv.gz
131 JU2565 JU2565 JU2565 BAM / BAI JU2565.20180527.tsv.gz
132 JU2566 JU2566 JU2566 BAM / BAI JU2566.20180527.tsv.gz
133 JU2570 JU2570 JU2570 BAM / BAI JU2570.20180527.tsv.gz
134 JU2572 JU2572 JU2572 BAM / BAI JU2572.20180527.tsv.gz
135 JU2575 JU2575 JU2575 BAM / BAI JU2575.20180527.tsv.gz
136 JU2576 JU2576 JU2576 BAM / BAI JU2576.20180527.tsv.gz
137 JU2578 JU2578 JU2578 BAM / BAI JU2578.20180527.tsv.gz
138 JU258 JU258 JU258 BAM / BAI JU258.20180527.tsv.gz
139 JU2581 JU2581 JU2581 BAM / BAI JU2581.20180527.tsv.gz
140 JU2586 JU2586 JU2586 BAM / BAI JU2586.20180527.tsv.gz
141 JU2587 JU2587 JU2587 BAM / BAI JU2587.20180527.tsv.gz
142 JU2592 JU2592 JU2592 BAM / BAI JU2592.20180527.tsv.gz
143 JU2593 JU2593 JU2593 BAM / BAI JU2593.20180527.tsv.gz
144 JU2600 JU2600 JU1924 JU2151 JU2600 JU3138 BAM / BAI JU2600.20180527.tsv.gz
145 JU2610 JU2610 JU2610 BAM / BAI JU2610.20180527.tsv.gz
146 JU2619 JU2619 JU2619 BAM / BAI JU2619.20180527.tsv.gz
147 JU2800 JU2800 JU2800 JU2802 BAM / BAI JU2800.20180527.tsv.gz
148 JU2811 JU2811 JU2811 BAM / BAI JU2811.20180527.tsv.gz
149 JU2825 JU2825 JU2825 BAM / BAI JU2825.20180527.tsv.gz
150 JU2829 JU2829 JU2828 JU2829 JU2830 BAM / BAI JU2829.20180527.tsv.gz
151 JU2838 JU2838 JU2838 BAM / BAI JU2838.20180527.tsv.gz
152 JU2841 JU2841 JU2841 BAM / BAI JU2841.20180527.tsv.gz
153 JU2853 JU2853 JU2853 BAM / BAI JU2853.20180527.tsv.gz
154 JU2862 JU2862 JU2862 BAM / BAI JU2862.20180527.tsv.gz
155 JU2866 JU2866 JU2866 BAM / BAI JU2866.20180527.tsv.gz
156 JU2878 JU2878 JU2878 BAM / BAI JU2878.20180527.tsv.gz
157 JU2879 JU2879 JU2879 BAM / BAI JU2879.20180527.tsv.gz
158 JU2906 JU2906 JU2906 BAM / BAI JU2906.20180527.tsv.gz
159 JU2907 JU2907 JU2907 JU2908 BAM / BAI JU2907.20180527.tsv.gz
160 JU310 JU310 JU1026 JU1037 JU1039 JU1040 JU1204 JU1206 JU262 JU263 JU299 JU300 JU301 JU302 JU303 JU305 JU306 JU307 JU309 JU310 JU438 BAM / BAI JU310.20180527.tsv.gz
161 JU311 JU311 ECA551 JU311 JU312 JU313 JU314 JU315 JU316 JU317 JU318 JU319 JU321 MY2481 BAM / BAI JU311.20180527.tsv.gz
162 JU3125 JU3125 JU3125 BAM / BAI JU3125.20180527.tsv.gz
163 JU3127 JU3127 JU3127 BAM / BAI JU3127.20180527.tsv.gz
164 JU3128 JU3128 JU3128 BAM / BAI JU3128.20180527.tsv.gz
165 JU3132 JU3132 JU3132 BAM / BAI JU3132.20180527.tsv.gz
166 JU3134 JU3134 JU3134 BAM / BAI JU3134.20180527.tsv.gz
167 JU3135 JU3135 JU3135 BAM / BAI JU3135.20180527.tsv.gz
168 JU3137 JU3137 JU3137 BAM / BAI JU3137.20180527.tsv.gz
169 JU3140 JU3140 JU3140 BAM / BAI JU3140.20180527.tsv.gz
170 JU3141 JU3141 JU3141 BAM / BAI JU3141.20180527.tsv.gz
171 JU3144 JU3144 JU3144 BAM / BAI JU3144.20180527.tsv.gz
172 JU3166 JU3166 JU3166 BAM / BAI JU3166.20180527.tsv.gz
173 JU3167 JU3167 JU3167 BAM / BAI JU3167.20180527.tsv.gz
174 JU3169 JU3169 JU3169 BAM / BAI JU3169.20180527.tsv.gz
175 JU3224 JU3224 JU3224 BAM / BAI JU3224.20180527.tsv.gz
176 JU3225 JU3225 JU3225 BAM / BAI JU3225.20180527.tsv.gz
177 JU3226 JU3226 JU3226 BAM / BAI JU3226.20180527.tsv.gz
178 JU3228 JU3228 JU3227 JU3228 BAM / BAI JU3228.20180527.tsv.gz
179 JU323 JU323 JU3131 JU322 JU323 JU342 JU347 BAM / BAI JU323.20180527.tsv.gz
180 JU3280 JU3280 JU3280 BAM / BAI JU3280.20180527.tsv.gz
181 JU3282 JU3282 JU3282 BAM / BAI JU3282.20180527.tsv.gz
182 JU3291 JU3291 JU3291 BAM / BAI JU3291.20180527.tsv.gz
183 JU346 JU346 JU345 JU346 BAM / BAI JU346.20180527.tsv.gz
184 JU360 JU360 JU360 JU362 JU363 JU364 JU366 JU368 JU369 JU370 JU801 BAM / BAI JU360.20180527.tsv.gz
185 JU367 JU367 JU361 JU367 JU371 JU692 JU693 JU694 BAM / BAI JU367.20180527.tsv.gz
186 JU393 JU393 JU393 BAM / BAI JU393.20180527.tsv.gz
187 JU394 JU394 JU394 JU399 JU400 BAM / BAI JU394.20180527.tsv.gz
188 JU397 JU397 JU397 JU398 JU401 JU402 BAM / BAI JU397.20180527.tsv.gz
189 JU406 JU406 JU406 JU407 BAM / BAI JU406.20180527.tsv.gz
190 JU440 JU440 JU440 BAM / BAI JU440.20180527.tsv.gz
191 JU561 JU561 JU561 JU563 BAM / BAI JU561.20180527.tsv.gz
192 JU642 JU642 JU642 BAM / BAI JU642.20180527.tsv.gz
193 JU751 JU751 JU751 BAM / BAI JU751.20180527.tsv.gz
194 JU774 JU774 JU774 BAM / BAI JU774.20180527.tsv.gz
195 JU775 JU775 JU775 JU799 BAM / BAI JU775.20180527.tsv.gz
196 JU778 JU778 JU778 BAM / BAI JU778.20180527.tsv.gz
197 JU782 JU782 JU782 BAM / BAI JU782.20180527.tsv.gz
198 JU792 JU792 JU2460 JU2527 JU3142 JU395 JU396 JU622 JU792 BAM / BAI JU792.20180527.tsv.gz
199 JU830 JU830 JU829 JU830 BAM / BAI JU830.20180527.tsv.gz
200 JU847 JU847 JU847 JU848 BAM / BAI JU847.20180527.tsv.gz
201 KR314 KR314 KR314 BAM / BAI KR314.20180527.tsv.gz
202 LKC34 LKC34 LKC34 BAM / BAI LKC34.20180527.tsv.gz
203 MY1 MY1 MY1 BAM / BAI MY1.20180527.tsv.gz
204 MY10 MY10 MY17 MY10 MY11 MY12 MY13 MY19 MY20 MY21 MY22 MY3 MY4 MY5 MY7 MY8 MY9 BAM / BAI MY10.20180527.tsv.gz
205 MY16 MY16 MY16 BAM / BAI MY16.20180527.tsv.gz
206 MY18 MY18 MY18 MY6 BAM / BAI MY18.20180527.tsv.gz
207 MY2147 MY2147 MY2143 MY2147 BAM / BAI MY2147.20180527.tsv.gz
208 MY2212 MY2212 MY2212 BAM / BAI MY2212.20180527.tsv.gz
209 MY23 MY23 BRC20231 JU1171 MY14 MY15 MY2 MY23 BAM / BAI MY23.20180527.tsv.gz
210 MY2453 MY2453 JU3136 MY2001 MY2004 MY2011 MY2014 MY2050 MY2051 MY2054 MY2121 MY2137 MY2199 MY2288 MY2339 MY2453 MY2502 MY2541 MY2579 MY2622 MY508 MY524 MY561 MY564 MY570 MY713 MY792 MY819 MY864 MY904 MY965 BAM / BAI MY2453.20180527.tsv.gz
211 MY2530 MY2530 MY2530 BAM / BAI MY2530.20180527.tsv.gz
212 MY2535 MY2535 MY2344 MY2532 MY2535 MY881 NIC508 NIC512 BAM / BAI MY2535.20180527.tsv.gz
213 MY2573 MY2573 ECA552 MY2142 MY2144 MY2198 MY2208 MY2224 MY2239 MY2282 MY2294 MY2338 MY2434 MY2443 MY2491 MY2573 MY559 MY579 MY710 MY804 MY934 NIC1604 BAM / BAI MY2573.20180527.tsv.gz
214 MY2585 MY2585 MY2585 MY2623 BAM / BAI MY2585.20180527.tsv.gz
215 MY2693 MY2693 MY2685 MY2693 MY2719 BAM / BAI MY2693.20180527.tsv.gz
216 MY2713 MY2713 MY2635 MY2679 MY2689 MY2713 MY803 BAM / BAI MY2713.20180527.tsv.gz
217 MY2741 MY2741 MY2109 MY2692 MY2741 BAM / BAI MY2741.20180527.tsv.gz
218 MY518 MY518 MY518 BAM / BAI MY518.20180527.tsv.gz
219 MY679 MY679 MY679 MY991 BAM / BAI MY679.20180527.tsv.gz
220 MY772 MY772 MY772 BAM / BAI MY772.20180527.tsv.gz
221 MY795 MY795 MY2099 MY538 MY673 MY795 BAM / BAI MY795.20180527.tsv.gz
222 MY920 MY920 MY2042 MY2097 MY2138 MY2347 MY2373 MY2406 MY2479 MY2688 MY589 MY741 MY887 MY920 MY990 BAM / BAI MY920.20180527.tsv.gz
223 N2 N2 ECA253 ECA254 ECA255 ECA257 N2 BAM / BAI N2.20180527.tsv.gz
224 NIC1 NIC1 NIC1 BAM / BAI NIC1.20180527.tsv.gz
225 NIC1049 NIC1049 NIC1049 BAM / BAI NIC1049.20180527.tsv.gz
226 NIC1107 NIC1107 NIC1107 BAM / BAI NIC1107.20180527.tsv.gz
227 NIC1119 NIC1119 NIC1119 BAM / BAI NIC1119.20180527.tsv.gz
228 NIC166 NIC166 NIC166 BAM / BAI NIC166.20180527.tsv.gz
229 NIC195 NIC195 NIC195 NIC196 NIC197 NIC198 BAM / BAI NIC195.20180527.tsv.gz
230 NIC199 NIC199 NIC199 NIC200 BAM / BAI NIC199.20180527.tsv.gz
231 NIC2 NIC2 NIC2 BAM / BAI NIC2.20180527.tsv.gz
232 NIC207 NIC207 NIC207 BAM / BAI NIC207.20180527.tsv.gz
233 NIC231 NIC231 NIC231 NIC232 BAM / BAI NIC231.20180527.tsv.gz
234 NIC236 NIC236 NIC236 NIC237 BAM / BAI NIC236.20180527.tsv.gz
235 NIC242 NIC242 NIC242 BAM / BAI NIC242.20180527.tsv.gz
236 NIC251 NIC251 NIC251 BAM / BAI NIC251.20180527.tsv.gz
237 NIC252 NIC252 NIC252 BAM / BAI NIC252.20180527.tsv.gz
238 NIC255 NIC255 NIC255 BAM / BAI NIC255.20180527.tsv.gz
239 NIC256 NIC256 NIC256 NIC263 BAM / BAI NIC256.20180527.tsv.gz
240 NIC258 NIC258 NIC258 BAM / BAI NIC258.20180527.tsv.gz
241 NIC259 NIC259 NIC259 BAM / BAI NIC259.20180527.tsv.gz
242 NIC260 NIC260 NIC260 BAM / BAI NIC260.20180527.tsv.gz
243 NIC261 NIC261 NIC261 BAM / BAI NIC261.20180527.tsv.gz
244 NIC262 NIC262 NIC262 BAM / BAI NIC262.20180527.tsv.gz
245 NIC265 NIC265 NIC265 BAM / BAI NIC265.20180527.tsv.gz
246 NIC266 NIC266 NIC266 BAM / BAI NIC266.20180527.tsv.gz
247 NIC267 NIC267 NIC267 NIC270 BAM / BAI NIC267.20180527.tsv.gz
248 NIC268 NIC268 NIC268 BAM / BAI NIC268.20180527.tsv.gz
249 NIC269 NIC269 NIC269 BAM / BAI NIC269.20180527.tsv.gz
250 NIC271 NIC271 NIC271 BAM / BAI NIC271.20180527.tsv.gz
251 NIC272 NIC272 NIC272 NIC273 BAM / BAI NIC272.20180527.tsv.gz
252 NIC274 NIC274 NIC274 BAM / BAI NIC274.20180527.tsv.gz
253 NIC275 NIC275 NIC275 BAM / BAI NIC275.20180527.tsv.gz
254 NIC276 NIC276 NIC276 BAM / BAI NIC276.20180527.tsv.gz
255 NIC277 NIC277 NIC277 BAM / BAI NIC277.20180527.tsv.gz
256 NIC3 NIC3 NIC3 NIC4 BAM / BAI NIC3.20180527.tsv.gz
257 NIC501 NIC501 NIC501 BAM / BAI NIC501.20180527.tsv.gz
258 NIC511 NIC511 NIC511 BAM / BAI NIC511.20180527.tsv.gz
259 NIC513 NIC513 NIC513 BAM / BAI NIC513.20180527.tsv.gz
260 NIC514 NIC514 NIC514 BAM / BAI NIC514.20180527.tsv.gz
261 NIC515 NIC515 NIC515 BAM / BAI NIC515.20180527.tsv.gz
262 NIC522 NIC522 NIC522 BAM / BAI NIC522.20180527.tsv.gz
263 NIC523 NIC523 NIC523 BAM / BAI NIC523.20180527.tsv.gz
264 NIC526 NIC526 NIC526 BAM / BAI NIC526.20180527.tsv.gz
265 NIC527 NIC527 NIC521 NIC527 BAM / BAI NIC527.20180527.tsv.gz
266 NIC528 NIC528 NIC528 BAM / BAI NIC528.20180527.tsv.gz
267 NIC529 NIC529 NIC529 BAM / BAI NIC529.20180527.tsv.gz
268 PB303 PB303 PB303 BAM / BAI PB303.20180527.tsv.gz
269 ECA259 PB306 ECA258 ECA259 BAM / BAI PB306.20180527.tsv.gz
270 PS2025 PS2025 PS2025 BAM / BAI PS2025.20180527.tsv.gz
271 PX179 PX179 PX178 PX179 BAM / BAI PX179.20180527.tsv.gz
272 QG2075 QG2075 QG2075 BAM / BAI QG2075.20180527.tsv.gz
273 QG2811 QG2811 QG2810 QG2811 BAM / BAI QG2811.20180527.tsv.gz
274 QG2813 QG2813 QG2812 QG2813 BAM / BAI QG2813.20180527.tsv.gz
275 QG2818 QG2818 QG2818 BAM / BAI QG2818.20180527.tsv.gz
276 QG2823 QG2823 QG2823 QG2826 BAM / BAI QG2823.20180527.tsv.gz
277 QG2824 QG2824 QG2824 BAM / BAI QG2824.20180527.tsv.gz
278 QG2825 QG2825 QG2825 BAM / BAI QG2825.20180527.tsv.gz
279 QG2827 QG2827 QG2827 QG2829 BAM / BAI QG2827.20180527.tsv.gz
280 QG2828 QG2828 QG2828 BAM / BAI QG2828.20180527.tsv.gz
281 QG2832 QG2832 QG2830 QG2831 QG2832 QG2833 BAM / BAI QG2832.20180527.tsv.gz
282 QG2835 QG2835 QG2834 QG2835 BAM / BAI QG2835.20180527.tsv.gz
283 QG2836 QG2836 QG2836 BAM / BAI QG2836.20180527.tsv.gz
284 QG2837 QG2837 QG2837 BAM / BAI QG2837.20180527.tsv.gz
285 QG2838 QG2838 QG2838 BAM / BAI QG2838.20180527.tsv.gz
286 QG2841 QG2841 QG2839 QG2840 QG2841 QG2842 BAM / BAI QG2841.20180527.tsv.gz
287 QG2843 QG2843 QG2843 BAM / BAI QG2843.20180527.tsv.gz
288 QG2846 QG2846 QG2844 QG2845 QG2846 BAM / BAI QG2846.20180527.tsv.gz
289 QG2850 QG2850 QG2850 QG2851 BAM / BAI QG2850.20180527.tsv.gz
290 QG2854 QG2854 QG2852 QG2853 QG2854 QG2856 QG2858 QG2859 BAM / BAI QG2854.20180527.tsv.gz
291 QG2855 QG2855 QG2855 BAM / BAI QG2855.20180527.tsv.gz
292 QG2857 QG2857 QG2857 BAM / BAI QG2857.20180527.tsv.gz
293 QG2873 QG2873 QG2872 QG2873 BAM / BAI QG2873.20180527.tsv.gz
294 QG2874 QG2874 QG2874 BAM / BAI QG2874.20180527.tsv.gz
295 QG2875 QG2875 QG2875 QG2876 BAM / BAI QG2875.20180527.tsv.gz
296 QG2877 QG2877 QG2877 QG2878 BAM / BAI QG2877.20180527.tsv.gz
297 QG2932 QG2932 QG2927 QG2928 QG2931 QG2932 BAM / BAI QG2932.20180527.tsv.gz
298 QG536 QG536 QG536 QG537 QG538 BAM / BAI QG536.20180527.tsv.gz
299 QG556 QG556 QG556 QG558 BAM / BAI QG556.20180527.tsv.gz
300 QG557 QG557 QG557 BAM / BAI QG557.20180527.tsv.gz
301 QW947 QW947 QW947 BAM / BAI QW947.20180527.tsv.gz
302 QX1211 QX1211 QX1211 QX1215 QX1216 BAM / BAI QX1211.20180527.tsv.gz
303 QX1212 QX1212 QX1212 QX1213 QX1214 BAM / BAI QX1212.20180527.tsv.gz
304 QX1233 QX1233 QX1218 QX1233 BAM / BAI QX1233.20180527.tsv.gz
305 QX1791 QX1791 QX1791 BAM / BAI QX1791.20180527.tsv.gz
306 QX1792 QX1792 QX1792 BAM / BAI QX1792.20180527.tsv.gz
307 QX1793 QX1793 QX1793 BAM / BAI QX1793.20180527.tsv.gz
308 QX1794 QX1794 QX1794 BAM / BAI QX1794.20180527.tsv.gz
309 RC301 RC301 MY2022 MY2024 MY2078 MY2291 MY2630 MY2636 MY2640 MY2681 MY2684 MY2691 MY684 MY882 RC301 BAM / BAI RC301.20180527.tsv.gz
310 WN2001 WN2001 WN2001 WN2010 WN2011 WN2013 WN2014 WN2016 WN2017 WN2018 WN2019 WN2020 WN2021 BAM / BAI WN2001.20180527.tsv.gz
311 WN2002 WN2002 WN2002 WN2003 BAM / BAI WN2002.20180527.tsv.gz
312 WN2033 WN2033 WN2033 WN2035 WN2039 BAM / BAI WN2033.20180527.tsv.gz
313 WN2050 WN2050 WN2050 WN2056 WN2062 BAM / BAI WN2050.20180527.tsv.gz
314 WN2063 WN2063 WN2063 BAM / BAI WN2063.20180527.tsv.gz
315 WN2064 WN2064 WN2064 BAM / BAI WN2064.20180527.tsv.gz
316 WN2066 WN2066 WN2059 WN2060 WN2065 WN2066 BAM / BAI WN2066.20180527.tsv.gz
317 XZ1513 XZ1513 XZ1513 BAM / BAI XZ1513.20180527.tsv.gz
318 XZ1514 XZ1514 XZ1514 BAM / BAI XZ1514.20180527.tsv.gz
319 XZ1515 XZ1515 XZ1515 BAM / BAI XZ1515.20180527.tsv.gz
320 XZ1516 XZ1516 XZ1516 BAM / BAI XZ1516.20180527.tsv.gz
321 XZ1672 XZ1672 XZ1672 BAM / BAI XZ1672.20180527.tsv.gz
322 XZ1734 XZ1734 XZ1734 BAM / BAI XZ1734.20180527.tsv.gz
323 XZ1735 XZ1735 XZ1735 BAM / BAI XZ1735.20180527.tsv.gz
324 XZ1756 XZ1756 XZ1756 BAM / BAI XZ1756.20180527.tsv.gz
325 XZ2018 XZ2018 XZ2018 BAM / BAI XZ2018.20180527.tsv.gz
326 XZ2019 XZ2019 XZ2019 BAM / BAI XZ2019.20180527.tsv.gz
327 XZ2020 XZ2020 XZ2020 BAM / BAI XZ2020.20180527.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 330 330
SNVs 3,396,485 2,493,687
Ts 1,900,352 1,392,602
Tv 1,623,877 1,101,085
Ts/Tv 1.17 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

Tajimas D

Click the above image to download the full version