Curious Very Long Snp In 1Kg Data

Question

[Click downvote]

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 ....

[Devon Ryan]

It does say SVTYPE=DEL, so...

[Click downvote]

But other snps look like: 20 3484167 rs143524500 A C ..., why such a long string?

[Pierre Lindenbaum]

why not ?

[Click downvote]

Because a SNP is one nucleotide (at least in my world)

[Pierre Lindenbaum]

no :-)

~$ curl -s "ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/00-All.vcf.gz" | gunzip -c | cut -f 1-5 | grep -v ',' | awk '(length($5)>100)'
1    2017221    rs70940712    C    CATGAGGTACCGTGCTGGAGGGGCTGAGGACGTCGGGGGGCCCTGTTCTCAGAGCCCTTGAGGCACCGTGCTGGAGGGGCTGAGGACGTCGGGGGGCCCTGTTCTCAGAGCCC
1    3611140    rs74221234    G    GCCCTGCAGCCTCCGCCCCTCCTCCCGCAATCCCAGCCCTGCAGCCTCCGCCCCTCCTCCCGCAATCCCAGCCCTGCAGCCTCAGCCCCTCCTCCTGCAATCCCAC

[Devon Ryan]

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 :)

[Click downvote]

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.

[Devon Ryan]

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 C or something like that, then it would only be the A that's deleted. In this case, there's a much larger region that's deleted.

[Devon Ryan]

Is that labeled as a structural variant?

Answer 1

[Devon Ryan]

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.