[chr12:16630818-16630993][INS][SVLEN=175bp]

[jzook]

chr12 16630818 Minda_24 N <INS> . PASS SVLEN=175;SVTYPE=INS;SUPP_VEC=ONT_severus_INS11657,ONT_Sniffles2.INS.D0MB,ONT_i_63,ONT_ID_20376_1,PB_severus_INS10178,PB_Sniffles2.INS.C5MB,PB_i_149

https://v2.genomeribbon.com/?session=https://42basepairs.com/download/s3/giab-data/ribbon-json/ribbon-hg008-cov-bedpe.json&locus=chr12:16630818#ribbon

[Faizal-Eeman]

• No other SVs 5Mbp upstream or downstream of this insertion
• This INS appears to have sequence similarity with a region in chr14

[Faizal-Eeman]

• This looks like a (AAAT)n repeat region

• The insertion sequence appears to be similar to the (AAAT)n repeat region

[Faizal-Eeman]

• BLAT results for the INS sequence shows multiple 100% sequence similarities with sequences from other chromosomes
• This could be a common repeat variant
• Therefore flagging this as a false call

[jo-mc]

Hi, nice work showing all the data.

If we look at the blat results, we need to consider the size field along with %. Here the top two matches are the only significant as they match ~148bp which is close to the length of the insert less the poly A tail. The remainder match only ~20-30bp. There are some characteristics of line-1 insertion due to target site duplication "AAAGATCAT" and poly -A tail. Also it is interesting that this is the third insert from the same region being intron 3 of Long non coding RNA, LINC01500.

[Faizal-Eeman]

If we look at the blat results, we need to consider the size field along with %. Here the top two matches are the only significant as they match ~148bp which is close to the length of the insert less the poly A tail. The remainder match only ~20-30bp.

Thanks @jo-mc I missed the size match. Also, replaced the previous image which showed the full BLAT results with just the top segment of the results.