Running mgpileup version 0.7
bam file                : testFiles/shortSorted.sam
reference sequence file : ../../bam/test/testFiles/chr1_partial.fa
output VCF file         : STDOUT
add deletions as bases  : no
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	-
1	75	.	A	.	.	.	.	N:BASE:MAPQ:BASEQ:STRAND:CYCLE:GL	1:A:0:26:F:1:0,3,3,3,30,30,30,30,30,30
1	76	.	C	.	.	.	.	N:BASE:MAPQ:BASEQ:STRAND:CYCLE:GL	1:C:0:29:F:2:33,3,33,33,0,3,3,33,33,33
1	77	.	T	.	.	.	.	N:BASE:MAPQ:BASEQ:STRAND:CYCLE:GL	1:G:0:29:F:3:33,33,3,33,33,3,33,0,3,33
1	78	.	T	.	.	.	.	N:BASE:MAPQ:BASEQ:STRAND:CYCLE:GL	1:T:0:29:F:4:33,33,33,3,33,33,3,33,3,0
1	79	.	N	.	.	.	.	N:BASE:MAPQ:BASEQ:STRAND:CYCLE:GL	1:N:0:29:F:5:0,0,0,0,0,0,0,0,0,0
2	75	.	N	.	.	.	.	N:BASE:MAPQ:BASEQ:STRAND:CYCLE:GL	1:A:0:32:F:1:0,3,3,3,36,36,36,36,36,36
2	76	.	N	.	.	.	.	N:BASE:MAPQ:BASEQ:STRAND:CYCLE:GL	1:C:0:32:F:2:36,3,36,36,0,3,3,36,36,36
2	77	.	N	.	.	.	.	N:BASE:MAPQ:BASEQ:STRAND:CYCLE:GL	1:G:0:32:F:3:36,36,3,36,36,3,36,0,3,36
2	78	.	N	.	.	.	.	N:BASE:MAPQ:BASEQ:STRAND:CYCLE:GL	1:T:0:32:F:4:36,36,36,3,36,36,3,36,3,0
2	79	.	N	.	.	.	.	N:BASE:MAPQ:BASEQ:STRAND:CYCLE:GL	1:N:0:32:F:5:0,0,0,0,0,0,0,0,0,0
2	1751	.	N	.	.	.	.	N:BASE:MAPQ:BASEQ:STRAND:CYCLE:GL	1:A:0:26:F:4:0,3,3,3,30,30,30,30,30,30
2	1752	.	N	.	.	.	.	N:BASE:MAPQ:BASEQ:STRAND:CYCLE:GL	1:C:0:29:F:5:33,3,33,33,0,3,3,33,33,33
2	1753	.	N	.	.	.	.	N:BASE:MAPQ:BASEQ:STRAND:CYCLE:GL	1:G:0:29:F:6:33,33,3,33,33,3,33,0,3,33
2	1754	.	N	.	.	.	.	N:BASE:MAPQ:BASEQ:STRAND:CYCLE:GL	1:T:0:29:F:7:33,33,33,3,33,33,3,33,3,0
2	1755	.	N	.	.	.	.	N:BASE:MAPQ:BASEQ:STRAND:CYCLE:GL	1:N:0:29:F:8:0,0,0,0,0,0,0,0,0,0
3	75	.	N	.	.	.	.	N:BASE:MAPQ:BASEQ:STRAND:CYCLE:GL	1:A:0:26:F:4:0,3,3,3,30,30,30,30,30,30
3	76	.	N	.	.	.	.	N:BASE:MAPQ:BASEQ:STRAND:CYCLE:GL	1:C:0:29:F:5:33,3,33,33,0,3,3,33,33,33
3	77	.	N	.	.	.	.	N:BASE:MAPQ:BASEQ:STRAND:CYCLE:GL	1:G:0:29:F:6:33,33,3,33,33,3,33,0,3,33
3	78	.	N	.	.	.	.	N:BASE:MAPQ:BASEQ:STRAND:CYCLE:GL	1:T:0:29:F:7:33,33,33,3,33,33,3,33,3,0
3	79	.	N	.	.	.	.	N:BASE:MAPQ:BASEQ:STRAND:CYCLE:GL	1:N:0:29:F:8:0,0,0,0,0,0,0,0,0,0
