Mismatch

Angsd can output mismatch count matrix from the reference given:

• - Distance from be beginning of the read (posi)
• - Distance from the end of the read (isop)
• - Strand
• - Qscore

Run like:

./angsd -i my.cram -ref hg19.fa -doMisMatch 1

Output looks like:

posi	isop	qs	strand	Ref	A	C	G	T
0	24	13	0	1	0	2	0	0
0	24	13	0	3	0	0	0	1
0	24	13	1	0	1	0	0	0
0	24	13	1	3	0	0	0	1
0	24	14	0	0	152	1	4	0
0	24	14	0	1	0	128	0	0
0	24	14	0	2	11	2	196	1
0	24	14	0	3	1	0	2	12
0	24	14	1	0	20	1	2	2
0	24	14	1	1	1	200	1	16
0	24	14	1	2	0	5	118	6
0	24	14	1	3	0	6	3	164
0	24	15	0	0	186	1	2	0
0	24	15	0	1	4	91	0	0
0	24	15	0	2	8	0	90	0
0	24	15	0	3	0	1	2	7
0	24	15	1	0	14	1	0	0
0	24	15	1	1	0	93	1	2
0	24	15	1	2	0	2	79	2

column 1 and colum two are the distance from each end of the read

qs is the quality score in numeric phred scale

Strand is which sequencing strand zero and one

Ref is the reference A,C,G,T = 0,1,2,3

The last 4 column is the count of bases acroos all reads where the position from the beginning is posi, distance from the end is isop, qualityscore is qs, strand is 0 or one.