There are nicer genomics visualization tools available, but the samtools tview
command is almost always my go-to for a quick first look at read alignments. I just brought up the following locus in tview
.
81055951 81055961 81055971 81055981 81055991 81056001 81056011 81056021
GTGGAGGTCGGCAGCAGAGCCTGTGGCAGCT**********************************************CTGAGGGTCGGCGTGGCCTCCTGGTGGAAGTTGCACCTGGTTTGCTT
............................... ...............................................
...............................**********************************************.. ......................................
,,,,,,,,,,,,,,,,,,,,,,,,,,,,**********************************************,, .....T................................
..... ,,,,,,,,**********************************************,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
....... ,,**********************************************,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
,,,,,,,,, ...............................................
............. .........................................A.....
........................ ...............................................
...............................**********************************************.. ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,**********************************************,, ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
...............................**********************************************.A...... ,,,,,,,,,,,,,,,,,,,,,,
...............................**********************************************.. ....................
,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,**********************************************,, ....................
,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,**********************************************,,,,,,,,,,,,,,,,,,,,,,,,,,,, ,,,,,,,,,,,,,,,
,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,**********************************************,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, ,,,,,
...............................**********************************************.. ,,,,,,,,,,,,,,
...............................**********************************************..
...............................**********************************************..
,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,**********************************************,,
,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,**********************************************,,
..................T............**********************************************...............................................
...............................**********************************************...............................................
...............................**********************************************...............................................
,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,**********************************************,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
...............................**********************************************...............................................
...............................**********************************************...............................................
,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,**********************************************,,
..............G................**********************************************...............................................
,,c,,,,,,,,,,,,,,,,,,,,,,,,,,,,**********************************************,,
...............................CTAAGCAAGTAACTGTGGTGTTAGAACCTACCTCCCTCGCCGGGCA...............................................
...............................**********************************************...............................................
...............................**********************************************........................................A......
...............................**********************************************...........................................T...
,,,,,,,,,,,,,,,,,,,,,g,,,,,,,,,**********************************************,,
,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,**********************************************,,
...............................................
...............................................
...............................................
,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,a,
,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
At first glance there appears to be only a single read spanning this insertion, although the abrupt end of many reads at the insertion breakpoints made me suspicious. Indeed, upon closer inspection, 19 additional reads have primary alignments with soft clipping at the insertion breakpoints.
By default, soft-clipped portions of the reads are not displayed. Is there any way to toggle this behavior?