Hello,
I have some confusion while interpreting 1000 genome project vcf file. For reference I am providing a portion of a row.
chr11
23934744
1kgp_3202_v38_ins_20
AGGTTCTCCACGTCCCCACCAGACTCAGGAGCCCAGCTGG
<INS:ME>
.
M
SVTYPE=ERV1;MEI=LTR12C;MEPRED=PASS;0START=23934744;1END=23934783;SVLEN=112;
Here what does 0START and 1END means? My point is if by giving start and end position it means that the TE covers this whole location then SVLEN should reflect this.
I am also assuming that the TE size is 112bp and it inserted into 23934744 location. Therefore, the END breakpoint or location is what making me confused.
Can anyone please help me clear things up?
Best,
Shovan