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Tandem repeat sequence too short at chr14_MATERNAL:107,224,612-107,233,706 #679

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nhansen opened this issue Apr 9, 2024 · 1 comment
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large_error This issue describes a poor quality or misassembled region in the assembly v1.0 This is an issue/error in the hg002v1.0 assembly

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@nhansen
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nhansen commented Apr 9, 2024

Have you confirmed that this issue hasn't already been reported?

  • I have confirmed in the UCSC browser hub that this is a new issue (required)

Issue location in assembly (use format chromosome:start-end, e.g., chr13_MATERNAL:3740148-9625296)

chr14_MATERNAL:107224612-107233706

Description of the issue

Sniffles predicts two insertions of about 100bp in this roughly 15kb-long 16bp tandem repeat, it likely sequence needs to be added to the assembly. It's hard to tell from the reads where the insertion should be, though:
image

@nhansen nhansen added v1.0 This is an issue/error in the hg002v1.0 assembly large_error This issue describes a poor quality or misassembled region in the assembly labels Apr 9, 2024
@nhansen
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nhansen commented Apr 9, 2024

The reads themselves show that there aren't really two locations with too few bases, but just one.

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Labels
large_error This issue describes a poor quality or misassembled region in the assembly v1.0 This is an issue/error in the hg002v1.0 assembly
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