Data

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Alignment Data

We aligned all wild isolate genomes to the WS245 version of the N2 genome. These data are stored using the BAM and CRAM formats. CRAM files are substantially smaller than BAM files.

Learn about alignment data here.

CRAM files are substantially smaller than BAM files, but require the reference to be converted to BAM files. We are currently using WS245 (Download).

Downloading All Alignment Data

Interested in downloading everything? Use the scripts below! Before these scripts 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.

Variant Data

We used samtools to identify single-nucleotide variant (SNV) sites as compared to the N2 reference genome (WS245). Variant data are provided as VCF or tab-delimited files.

Learn more about VCF files here.

VCF

The file below is a single VCF containing SNVs for all wild isolates.

WI.20160408.vcf.gz

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

Methods

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


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 BAM CRAM Tab-delimited variants
1 AB1 AB1 AB1 AB1.bam / .bai AB1.cram / .crai AB1.20160408.tsv
2 BRC20067 BRC20067 BRC20067 BRC20067.bam / .bai BRC20067.cram / .crai BRC20067.20160408.tsv
3 ECA243 CB4851 DR1344 ECA243 RW7000 CB4851.bam / .bai CB4851.cram / .crai CB4851.20160408.tsv
4 CB4852 CB4852 CB4852 JU1563 CB4852.bam / .bai CB4852.cram / .crai CB4852.20160408.tsv
5 ECA246 CB4853 CB3198 DR1350 ECA245 ECA246 CB4853.bam / .bai CB4853.cram / .crai CB4853.20160408.tsv
6 CB4854 CB4854 CB3196 CB3197 CB4854 CB4854.bam / .bai CB4854.cram / .crai CB4854.20160408.tsv
7 ECA248 CB4855 ECA248 CB4855.bam / .bai CB4855.cram / .crai CB4855.20160408.tsv
8 CB4856 CB4856 CB4856 ECA260 CB4856.bam / .bai CB4856.cram / .crai CB4856.20160408.tsv
9 ECA250 CB4857 CB3199 DR1345 ECA249 ECA250 CB4857.bam / .bai CB4857.cram / .crai CB4857.20160408.tsv
10 ECA251 CB4858 AB2 AB3 AB4 CX11258 CX11278 CX11305 CX11317 ECA247 ECA251 CB4858.bam / .bai CB4858.cram / .crai CB4858.20160408.tsv
11 CB4932 CB4932 CB4932 CB4932.bam / .bai CB4932.cram / .crai CB4932.20160408.tsv
12 CX11254 CX11254 CX11254 CX11254.bam / .bai CX11254.cram / .crai CX11254.20160408.tsv
13 CX11262 CX11262 CX11262 CX11294 CX11262.bam / .bai CX11262.cram / .crai CX11262.20160408.tsv
14 CX11264 CX11264 CX11264 CX11264.bam / .bai CX11264.cram / .crai CX11264.20160408.tsv
15 CX11271 CX11271 CX11271 CX11319 CX11271.bam / .bai CX11271.cram / .crai CX11271.20160408.tsv
16 CX11276 CX11276 CX11276 CX11316 CX11276.bam / .bai CX11276.cram / .crai CX11276.20160408.tsv
17 CX11285 CX11285 CX11285 CX11321 CX11285.bam / .bai CX11285.cram / .crai CX11285.20160408.tsv
18 CX11292 CX11292 CX11259 CX11292 CX11292.bam / .bai CX11292.cram / .crai CX11292.20160408.tsv
19 CX11307 CX11307 CX11307 CX11307.bam / .bai CX11307.cram / .crai CX11307.20160408.tsv
20 CX11314 CX11314 CX11314 CX11314.bam / .bai CX11314.cram / .crai CX11314.20160408.tsv
21 CX11315 CX11315 CX11268 CX11315 CX11315.bam / .bai CX11315.cram / .crai CX11315.20160408.tsv
22 DL200 DL200 DL200 DL200.bam / .bai DL200.cram / .crai DL200.20160408.tsv
23 DL226 DL226 DL226 DL226.bam / .bai DL226.cram / .crai DL226.20160408.tsv
24 DL238 DL238 DL238 DL238.bam / .bai DL238.cram / .crai DL238.20160408.tsv
25 ECA252 ECA252 ECA252 ECA252.bam / .bai ECA252.cram / .crai ECA252.20160408.tsv
26 ECA36 ECA36 ECA36 ECA36.bam / .bai ECA36.cram / .crai ECA36.20160408.tsv
27 ED3005 ED3005 ED3005 ED3021 ED3005.bam / .bai ED3005.cram / .crai ED3005.20160408.tsv
28 ED3011 ED3011 ED3011 ED3011.bam / .bai ED3011.cram / .crai ED3011.20160408.tsv
29 ED3012 ED3012 ED3010 ED3012 ED3014 ED3015 ED3023 ED3024 ED3028 ED3012.bam / .bai ED3012.cram / .crai ED3012.20160408.tsv
30 ED3017 ED3017 ED3017 ED3019 ED3020 ED3017.bam / .bai ED3017.cram / .crai ED3017.20160408.tsv
31 ED3040 ED3040 ED3040 ED3040.bam / .bai ED3040.cram / .crai ED3040.20160408.tsv
32 ED3046 ED3046 ED3046 ED3046.bam / .bai ED3046.cram / .crai ED3046.20160408.tsv
33 ED3048 ED3048 ED3042 ED3048 ED3048.bam / .bai ED3048.cram / .crai ED3048.20160408.tsv
34 ED3049 ED3049 ED3049 ED3049.bam / .bai ED3049.cram / .crai ED3049.20160408.tsv
35 ED3052 ED3052 ED3043 ED3052 ED3052.bam / .bai ED3052.cram / .crai ED3052.20160408.tsv
36 ED3073 ED3073 ED3057 ED3072 ED3073 ED3075 ED3073.bam / .bai ED3073.cram / .crai ED3073.20160408.tsv
37 ED3077 ED3077 ED3077 ED3077.bam / .bai ED3077.cram / .crai ED3077.20160408.tsv
38 EG4347 EG4347 EG4346 EG4347 EG4347.bam / .bai EG4347.cram / .crai EG4347.20160408.tsv
39 EG4349 EG4349 EG4348 EG4349 EG4349.bam / .bai EG4349.cram / .crai EG4349.20160408.tsv
40 EG4724 EG4724 EG4724 EG4724.bam / .bai EG4724.cram / .crai EG4724.20160408.tsv
41 EG4725 EG4725 EG4725 EG4725.bam / .bai EG4725.cram / .crai EG4725.20160408.tsv
42 EG4946 EG4946 EG4680 EG4689 EG4945 EG4946 EG4948 EG4951 EG4957 EG4946.bam / .bai EG4946.cram / .crai EG4946.20160408.tsv
43 GXW1 GXW1 GXW1 GXW1.bam / .bai GXW1.cram / .crai GXW1.20160408.tsv
44 JT11398 JT11398 JT11362 JT11398 JT11399 JT11398.bam / .bai JT11398.cram / .crai JT11398.20160408.tsv
45 JU1088 JU1088 JU1088 JU1088.bam / .bai JU1088.cram / .crai JU1088.20160408.tsv
46 JU1172 JU1172 JU1172 JU1172.bam / .bai JU1172.cram / .crai JU1172.20160408.tsv
47 JU1200 JU1200 JU1200 JU1200.bam / .bai JU1200.cram / .crai JU1200.20160408.tsv
48 JU1212 JU1212 JU1207 JU1212 JU1214 JU1212.bam / .bai JU1212.cram / .crai JU1212.20160408.tsv
49 JU1213 JU1213 JU1213 JU1482 JU531 JU533 JU1213.bam / .bai JU1213.cram / .crai JU1213.20160408.tsv
50 JU1242 JU1242 JU1242 JU1243 JU1218 JU1230 JU1242.bam / .bai JU1242.cram / .crai JU1242.20160408.tsv
51 JU1246 JU1246 JU1246 JU1246.bam / .bai JU1246.cram / .crai JU1246.20160408.tsv
52 JU1395 JU1395 JU1395 ECA589 JU1395.bam / .bai JU1395.cram / .crai JU1395.20160408.tsv
53 JU1400 JU1400 JU1400 JU1400.bam / .bai JU1400.cram / .crai JU1400.20160408.tsv
54 JU1409 JU1409 JU1401 JU1409 JU1410 JU1411 JU1409.bam / .bai JU1409.cram / .crai JU1409.20160408.tsv
55 JU1440 JU1440 JU1440 JU1440.bam / .bai JU1440.cram / .crai JU1440.20160408.tsv
56 JU1491 JU1491 JU1484 JU1491 JU1491.bam / .bai JU1491.cram / .crai JU1491.20160408.tsv
57 JU1530 JU1530 JU1530 ECA616 JU1530.bam / .bai JU1530.cram / .crai JU1530.20160408.tsv
58 JU1568 JU1568 JU1566 JU1568 JU1568.bam / .bai JU1568.cram / .crai JU1568.20160408.tsv
59 JU1580 JU1580 JU1580 JU1580.bam / .bai JU1580.cram / .crai JU1580.20160408.tsv
60 JU1581 JU1581 JU1511 JU1516 JU1522 JU1581 JU1582 JU1581.bam / .bai JU1581.cram / .crai JU1581.20160408.tsv
61 JU1586 JU1586 JU1586 JU1586.bam / .bai JU1586.cram / .crai JU1586.20160408.tsv
62 JU1652 JU1652 JU1652 JU1652.bam / .bai JU1652.cram / .crai JU1652.20160408.tsv
63 JU1896 JU1896 JU1896 JU1896.bam / .bai JU1896.cram / .crai JU1896.20160408.tsv
64 JU2001 JU2001 JU2001 JU2001.bam / .bai JU2001.cram / .crai JU2001.20160408.tsv
65 JU2007 JU2007 JU2007 JU2007.bam / .bai JU2007.cram / .crai JU2007.20160408.tsv
66 JU2316 JU2316 JU2316 JU2316.bam / .bai JU2316.cram / .crai JU2316.20160408.tsv
67 JU2464 JU2464 JU2464 JU2467 JU2468 JU2464.bam / .bai JU2464.cram / .crai JU2464.20160408.tsv
68 JU2466 JU2466 JU2466 JU2466.bam / .bai JU2466.cram / .crai JU2466.20160408.tsv
69 JU2513 JU2513 JU2513 JU2513.bam / .bai JU2513.cram / .crai JU2513.20160408.tsv
70 JU2519 JU2519 JU2519 JU2519.bam / .bai JU2519.cram / .crai JU2519.20160408.tsv
71 JU2522 JU2522 JU2522 JU2522.bam / .bai JU2522.cram / .crai JU2522.20160408.tsv
72 JU2526 JU2526 JU2526 JU2526.bam / .bai JU2526.cram / .crai JU2526.20160408.tsv
73 JU258 JU258 JU258 JU258.bam / .bai JU258.cram / .crai JU258.20160408.tsv
74 JU310 JU310 JU1026 JU1037 JU1039 JU1040 JU1204 JU1206 JU262 JU263 JU299 JU300 JU301 JU302 JU303 JU305 JU306 JU307 JU309 JU310 JU438 JU310.bam / .bai JU310.cram / .crai JU310.20160408.tsv
75 JU311 JU311 JU311 JU312 JU313 JU314 JU315 JU316 JU317 JU318 JU319 JU321 JU311.bam / .bai JU311.cram / .crai JU311.20160408.tsv
76 JU323 JU323 JU322 JU323 JU342 JU347 JU323.bam / .bai JU323.cram / .crai JU323.20160408.tsv
77 JU346 JU346 JU346 JU346.bam / .bai JU346.cram / .crai JU346.20160408.tsv
78 JU360 JU360 JU360 JU362 JU363 JU364 JU366 JU368 JU369 JU370 JU801 JU360.bam / .bai JU360.cram / .crai JU360.20160408.tsv
79 JU367 JU367 JU361 JU367 JU371 JU692 JU693 JU694 JU367.bam / .bai JU367.cram / .crai JU367.20160408.tsv
80 JU393 JU393 JU393 JU393.bam / .bai JU393.cram / .crai JU393.20160408.tsv
81 JU394 JU394 JU394 JU399 JU400 JU394.bam / .bai JU394.cram / .crai JU394.20160408.tsv
82 JU397 JU397 JU397 JU398 JU401 JU402 JU397.bam / .bai JU397.cram / .crai JU397.20160408.tsv
83 JU406 JU406 JU406 JU407 JU406.bam / .bai JU406.cram / .crai JU406.20160408.tsv
84 JU440 JU440 JU440 JU440.bam / .bai JU440.cram / .crai JU440.20160408.tsv
85 JU561 JU561 JU561 JU563 JU561.bam / .bai JU561.cram / .crai JU561.20160408.tsv
86 JU642 JU642 JU642 JU642.bam / .bai JU642.cram / .crai JU642.20160408.tsv
87 JU751 JU751 JU751 JU751.bam / .bai JU751.cram / .crai JU751.20160408.tsv
88 JU774 JU774 JU774 JU774.bam / .bai JU774.cram / .crai JU774.20160408.tsv
89 JU775 JU775 JU775 JU799 JU775.bam / .bai JU775.cram / .crai JU775.20160408.tsv
90 JU778 JU778 JU778 JU778.bam / .bai JU778.cram / .crai JU778.20160408.tsv
91 JU782 JU782 JU782 JU782.bam / .bai JU782.cram / .crai JU782.20160408.tsv
92 JU792 JU792 JU395 JU396 JU622 JU792 JU792.bam / .bai JU792.cram / .crai JU792.20160408.tsv
93 JU830 JU830 JU829 JU830 JU830.bam / .bai JU830.cram / .crai JU830.20160408.tsv
94 JU847 JU847 JU847 JU848 JU847.bam / .bai JU847.cram / .crai JU847.20160408.tsv
95 KR314 KR314 KR314 KR314.bam / .bai KR314.cram / .crai KR314.20160408.tsv
96 LKC34 LKC34 LKC34 LKC34.bam / .bai LKC34.cram / .crai LKC34.20160408.tsv
97 LSJ1 LSJ1 LSJ1 LSJ1.bam / .bai LSJ1.cram / .crai LSJ1.20160408.tsv
98 MY1 MY1 MY1 MY1.bam / .bai MY1.cram / .crai MY1.20160408.tsv
99 MY10 MY10 MY10 MY11 MY12 MY13 MY17 MY19 MY20 MY21 MY22 MY3 MY4 MY5 MY7 MY8 MY9 MY10.bam / .bai MY10.cram / .crai MY10.20160408.tsv
100 MY16 MY16 MY16 MY16.bam / .bai MY16.cram / .crai MY16.20160408.tsv
101 MY18 MY18 MY18 MY6 MY18.bam / .bai MY18.cram / .crai MY18.20160408.tsv
102 MY23 MY23 JU1171 MY14 MY15 MY2 MY23 MY23.bam / .bai MY23.cram / .crai MY23.20160408.tsv
103 N2 N2 CB3191 CB3192 CB3193 CB3194 CB3195 CB4507 ECA244 ECA253 ECA254 ECA255 ECA257 N2 PX176 TR388 TR389 N2.bam / .bai N2.cram / .crai N2.20160408.tsv
104 NIC1 NIC1 NIC1 NIC1.bam / .bai NIC1.cram / .crai NIC1.20160408.tsv
105 NIC166 NIC166 NIC166 NIC166.bam / .bai NIC166.cram / .crai NIC166.20160408.tsv
106 NIC195 NIC195 NIC195 NIC196 NIC197 NIC198 NIC195.bam / .bai NIC195.cram / .crai NIC195.20160408.tsv
107 NIC199 NIC199 NIC199 NIC200 NIC199.bam / .bai NIC199.cram / .crai NIC199.20160408.tsv
108 NIC2 NIC2 NIC2 NIC2.bam / .bai NIC2.cram / .crai NIC2.20160408.tsv
109 NIC207 NIC207 NIC207 NIC207.bam / .bai NIC207.cram / .crai NIC207.20160408.tsv
110 NIC231 NIC231 NIC231 NIC232 NIC231.bam / .bai NIC231.cram / .crai NIC231.20160408.tsv
111 NIC236 NIC236 NIC236 NIC237 NIC236.bam / .bai NIC236.cram / .crai NIC236.20160408.tsv
112 NIC242 NIC242 NIC242 NIC242.bam / .bai NIC242.cram / .crai NIC242.20160408.tsv
113 NIC251 NIC251 NIC251 NIC251.bam / .bai NIC251.cram / .crai NIC251.20160408.tsv
114 NIC252 NIC252 NIC252 NIC252.bam / .bai NIC252.cram / .crai NIC252.20160408.tsv
115 NIC255 NIC255 NIC255 NIC255.bam / .bai NIC255.cram / .crai NIC255.20160408.tsv
116 NIC256 NIC256 NIC256 NIC263 NIC256.bam / .bai NIC256.cram / .crai NIC256.20160408.tsv
117 NIC258 NIC258 NIC258 NIC258.bam / .bai NIC258.cram / .crai NIC258.20160408.tsv
118 NIC259 NIC259 NIC259 NIC259.bam / .bai NIC259.cram / .crai NIC259.20160408.tsv
119 NIC260 NIC260 NIC260 NIC260.bam / .bai NIC260.cram / .crai NIC260.20160408.tsv
120 NIC261 NIC261 NIC261 NIC261.bam / .bai NIC261.cram / .crai NIC261.20160408.tsv
121 NIC262 NIC262 NIC262 NIC262.bam / .bai NIC262.cram / .crai NIC262.20160408.tsv
122 NIC265 NIC265 NIC265 NIC265.bam / .bai NIC265.cram / .crai NIC265.20160408.tsv
123 NIC266 NIC266 NIC266 NIC266.bam / .bai NIC266.cram / .crai NIC266.20160408.tsv
124 NIC267 NIC267 NIC267 NIC270 NIC267.bam / .bai NIC267.cram / .crai NIC267.20160408.tsv
125 NIC268 NIC268 NIC268 NIC268.bam / .bai NIC268.cram / .crai NIC268.20160408.tsv
126 NIC269 NIC269 NIC269 NIC269.bam / .bai NIC269.cram / .crai NIC269.20160408.tsv
127 NIC271 NIC271 NIC271 NIC271.bam / .bai NIC271.cram / .crai NIC271.20160408.tsv
128 NIC272 NIC272 NIC272 NIC273 NIC272.bam / .bai NIC272.cram / .crai NIC272.20160408.tsv
129 NIC274 NIC274 NIC274 NIC274.bam / .bai NIC274.cram / .crai NIC274.20160408.tsv
130 NIC275 NIC275 NIC275 NIC275.bam / .bai NIC275.cram / .crai NIC275.20160408.tsv
131 NIC276 NIC276 NIC276 NIC276.bam / .bai NIC276.cram / .crai NIC276.20160408.tsv
132 NIC277 NIC277 NIC277 NIC277.bam / .bai NIC277.cram / .crai NIC277.20160408.tsv
133 NIC3 NIC3 NIC3 NIC4 NIC3.bam / .bai NIC3.cram / .crai NIC3.20160408.tsv
134 PB303 PB303 PB303 PB303.bam / .bai PB303.cram / .crai PB303.20160408.tsv
135 ECA259 PB306 ECA258 ECA259 PB306.bam / .bai PB306.cram / .crai PB306.20160408.tsv
136 PS2025 PS2025 PS2025 PS2025.bam / .bai PS2025.cram / .crai PS2025.20160408.tsv
137 PX179 PX179 PX178 PX179 PX179.bam / .bai PX179.cram / .crai PX179.20160408.tsv
138 QG2075 QG2075 QG2075 QG2075.bam / .bai QG2075.cram / .crai QG2075.20160408.tsv
139 QG536 QG536 QG536 QG537 QG538 QG536.bam / .bai QG536.cram / .crai QG536.20160408.tsv
140 QG556 QG556 QG556 QG558 QG556.bam / .bai QG556.cram / .crai QG556.20160408.tsv
141 QG557 QG557 QG557 QG557.bam / .bai QG557.cram / .crai QG557.20160408.tsv
142 QW947 QW947 QW947 QW947.bam / .bai QW947.cram / .crai QW947.20160408.tsv
143 QX1211 QX1211 QX1211 QX1215 QX1216 QX1211.bam / .bai QX1211.cram / .crai QX1211.20160408.tsv
144 QX1212 QX1212 QX1212 QX1213 QX1214 QX1212.bam / .bai QX1212.cram / .crai QX1212.20160408.tsv
145 QX1233 QX1233 QX1218 QX1233 QX1233.bam / .bai QX1233.cram / .crai QX1233.20160408.tsv
146 QX1791 QX1791 QX1791 QX1791.bam / .bai QX1791.cram / .crai QX1791.20160408.tsv
147 QX1792 QX1792 QX1792 QX1792.bam / .bai QX1792.cram / .crai QX1792.20160408.tsv
148 QX1793 QX1793 QX1793 QX1793.bam / .bai QX1793.cram / .crai QX1793.20160408.tsv
149 QX1794 QX1794 QX1794 QX1794.bam / .bai QX1794.cram / .crai QX1794.20160408.tsv
150 RC301 RC301 PX174 RC301 RC301.bam / .bai RC301.cram / .crai RC301.20160408.tsv
151 WN2001 WN2001 WN2001 WN2010 WN2011 WN2013 WN2014 WN2016 WN2017 WN2018 WN2019 WN2020 WN2021 WN2001.bam / .bai WN2001.cram / .crai WN2001.20160408.tsv
152 WN2002 WN2002 WN2002 WN2003 WN2002.bam / .bai WN2002.cram / .crai 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



1.1.2