Meaning Of Colors Used In Samtools Tview

Question

[deepthithomaskannan]

Hi all,

When we use samtools tview the reference sequence appears in different colors. From the help window we can infer that different colors indicates quality of alignment. In my file one read is exact match with the reference sequence. But the reference sequence has shown in blue color which indicates the quality is very low. Anyone has any idea about the color coding used in samtools tview?

Thanks, Deeps

[Zev.Kronenberg]

For color coding information type '?' in tview. As for why the reference sequence has colors, IDK.