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IGV related questions

  1. May I know what is the triangle icon (between coverage and track file) in the IGV represent? enter image description here

  2. May I know what is the count below means? From my understanding, for that particular base position, there is 222 reads with G aligned to the reference at that particular position. However, why there is 136 'N' count when PacBio subreads were used to map against reference?

What is the detail explanation on the 7 deletion and 136 insertion as shown below? 

Total count: 222
A : 0
C : 0
G : 86 (39%, 38+, 48- )
T : 0
N : 136 (61%, 72+, 64- )
---------------
DEL: 7
INS: 136
alignment
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by wes • wes

1 answer

1) May I know what is the triangle icon

I would say that these are insertion markers ( https://github.com/igvteam/igv/blob/777506b0ec539fc718d5649a094efae9e735ca16/src/main/java/org/broad/igv/sam/AlignmentTrack.java#L617 )

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written by Pierre Lindenbaum Pierre Lindenbaum

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