Curious Very Long Snp In 1Kg Data
From the 20. chromosome of the finnish samples in 1000 genomes. What is this monster string supposed to be? There are several others like it so it is unlikely to be a mistake.
20 348416 esv2677012 CCTAAGCCCTCCCCACAGCTACCACCCTATTTTTTCTCCCCTTTGCAGAAAAGGGCTTTGAGAAAATTGTCTATCCTCGCTGTTTTTAATTAGTCTTCTCTCTCTCTCTCCCTCTGAGACAGGATCTGCTCTCTCACCCAAGCTGGAGTGCAGTGGCGTGATCATGGCTCACTGCAGCCTCAACCTCCTGGGCTCAAACGATCTTCCCACCTCAGCCTCCTGAGTAGCTGGGACTACAGGTGTGCACTACCATGCCTGGCTAATTTTTGTATTTTTTGTAGAGACTGGGTTTTGCCATGTTGCCCAGGCTGGTTTTGAACTCCCAGGCTCAAGTGATCCATCCACCTCAGCCTCCCAAAGTGCTGGGACTGCAGGTGTGAGCCACCACACCTGGCCCTCTTGTCTCTTAAGTCCATTTAATCATGCTTCTACCTGTCACTTCCCTAGTTGAAACTGCTCTTGTCAATTTCAACACATTGCTAAATCCAATGTGTTCAGTTCTCATTCTTCATCTTTTTTTTTTTTTTTTTTTGAGACAGAGTCTTGCTCTGTCACCCAGGCTGGAATACAGTGGCACGATCTTGGCCCACTGCAACCTCTGCCTCCTGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGTTGGGACTACAGGCACAAGCCACCAAACCCAGCTAATTTTTGTATTTTTAGTTGAGACGGCATTTCACCATGTTGGCCAGGATGGTCTCAATCTCTTGACCTCGTGATCCGCCCACCTTGGCCTCCAAAAGTGCTGGGATTACAGGTGTGAGCCACCGCACCCGGCCCATTCTTCATCTTCTTAACTGATCAACAGTTTGACACAGCTGACCACTCCCTGCTCTTTGATGTACTTCTTTTCACTTGGTGGCCAGGCCTCCACTCTCTGCTGGTTTTCCTCCTTCTCAGGCTCCCTGCTTCTCCCATTCCTGTTGGAGCAGTGAGGACTTGGTCCCTGGAGCTCTCATCCAGTCTCACGTCTATGACTCCCAACACTGTATCCTCAGCCCAGACCTCTCCCCTGAACTCCAGCCCATACATTCAAATACCTACCTGATGTCTCTTTGAGGATGTCAAAAGACATGACAGACTCCACAGAACCAAAGCTGAACCTGGGCTTCCCCCAAACACCTCGCTCCATGTCATTTGATGGCAGTTCCATACCTGTCACCGTTCAGGCCAAGAAACCTTGGAAGCACCTTGACACCTCCTTTTCCCTCAAACTCCACATCTAGACCATCAGCAATCCTGTTGGCTCCACCTTTAAAATATACCCAGAATCCAGTCACAGCTCACCTCTAGCATGGCCACTGCCCTGCTCTGAGCCACTGGAGTTTAAGAGAATTATTGCAACACCTGCTCCCTTGTCTTCCTGTCCTTGCCTCATTCAGTCTATTCCAAGTACAGATCCCTAAATGATTTTATTTTAAAAGTAAGTCAAGGCTGGGCATGGTAGCTCATGCCTGTAATCCTAGCGCTTGAGGAGGCCGAGGAAGGAGGATCACTTGGGTGTAGGAGTTTGAGACCCACCTGGGCAATGTGGCAAAACCCTGTCTGTACTTAAAAAAAAGAAAAAAAATGGCTGGGCATGGTGGCTCACCCTGTAATCTTAGCACTTTGGGAGGCTGAGGCGGGTGAATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGATGAAACCCCATCTCTACTAAAAATACAAAAATTAGCCGGGCAAGGTGATGCACGCCTGTAGTCCCAGCTACTCAGGAGGCTAAGGAAGAAGAATCACTGGAACCCAGGAGGTGGAGGTTGCAGTGAGCCAAGATCGCGCCACTGCACTCCAGCCTGCATGACAGGAGCGAGACTCCATCTCAAAAAAAAAAAAAAAAAAAAAAAGGTAAGTGAGATCACTTCCCTCCTCTCCTTAAACCCTCCCCTGCCTCCCCATGACTCCTCAGCGTCCTTTCAAAGGCCTCCAAAGCTCCAGATTATCTGAACCCCCTTTACCTCTCTGACCTCATCTCCCACCGCCTCCCTGTCACTGGCTGCACTCCAGCCACATTGACCTTCTCCGATGGCACACCAGTCAGCTAGTCAGCTTCCTTTTGGAGCTTTTGCATGAGCTGTTCCTCTTCCTGAAGAATTTGCCCTTCGGATAGTCTCAGGGCATCCACTGAACACTCCACTCAATACAGCCACTGCCTGCCCACCCAACACTCCTCATCTCTGTACTTACTCTTTTTTTCCCTTGCATTCGTCACCCCCTAACATGTGCTACAATGTACTTATTATGGTAATTATTTCTTGCATGTTTCTTTCTTTTTTTTTTTGAGACAGGGTCTCACTCTGTTGCCCAGTCTGGAGTGCAGCAGCATGATCTCAGCTCACTGAAATCTTGGCCTACCTGGCTCAGGCCATCCTCCCTCCTCTGCCTCCTGAGTAGCTGGGACTACAGGCACTCACCACCATGCCTGGCTAGTTGTTGTACTTTTTTGTAGAGATGAGGTTTCACCATGTTGCCTAAGCTAGTCTAAAACTCCTAGGCTCAAGTGATCCTCCCGCCTCAGCCTCCCGAAGTACTGGGATTGCGGGTGTGAGCCGCTGTGCCTGGCTGCACTTTTCCTTCTAATGGAATGTAAGCGCCACTTTTGTCTGTTATTTTCA C . PASS AC=0;AF=0.0032;AFR_AF=0.01;AN=186;AVGPOST=0.9985;CIEND=-67,86;CIPOS=-69,88;END=351092;ERATE=0.0004;EUR_AF=0.0013;HOMLEN=2;HOMSEQ=CT;LDAF=0.0032;RSQ=0.8232;SVLEN=-2676;SVTYPE=DEL;THETA=0.0246;VT=SV GT:DS:GL 0|0:0.000:-0.00,-3.63,-71.20 0|0:0.000:-0.01,-1.70,-50.53 ....
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1 answer
As mentioned in the comments, there are a number of different type of variations contained within that file. Some of these are simple SNPs, which would have much shorter lines. Others are larger structural variations, such as the one in your example, which happens to represent a deletion.
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It does say
SVTYPE=DEL, so...But other snps look like: 20 3484167 rs143524500 A C ..., why such a long string?
why not ?
Because a SNP is one nucleotide (at least in my world)
And the example in your original post is considered a SNP in your world? I think not.
Edit: In other words, reread and then understand my first comment and you'll know why this is the way it is :)
Okay, so these files aren't just SNPs, but also structural variation. Write that comment up as a (short) answer and I'll accept and upvote. Ps. I still do not understand why a deletion is described with such a long string.
Done. The deletion is described as such a long string so it's clear what's actually being deleted. If the line were just
20 348416 esv2677012 CA Cor something like that, then it would only be theAthat's deleted. In this case, there's a much larger region that's deleted.no :-)
Is that labeled as a structural variant?