what do read with blue outline represent in IGV?

Dumb question, but I can't seem to find the answer in the IGV docs. I am unable to upload a screenshot due to restrictions, but I am viewing my alignments of Illumina PE reads aligned with BWA mem. Do the reads with a blue outline indicate improper insert size?

igv alignment

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updated 9.5 years ago by Biomonika (Noolean)

• written 9.5 years ago by aindap

2 answers

Could this page help?

for an inferred insert size that is smaller than expected (insertion) igv/interpreting_insert_size

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written 9.5 years ago by Biomonika (Noolean)

As far as I know the blue read indicate read from forward strand, red - reverse, grey - both.

Best,

Agata

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written 9.5 years ago by agata88

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