Question: IGV related questions
0
gravatar for wes
18 days ago by
wes40
wes40 wrote:
  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 • 143 views
ADD COMMENTlink modified 18 days ago by Pierre Lindenbaum133k • written 18 days ago by wes40
1
gravatar for Pierre Lindenbaum
18 days ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum133k wrote:

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 )

ADD COMMENTlink written 18 days ago by Pierre Lindenbaum133k
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