for i in *bam
> do
> echo $i
> samtools flagstat $i
> done
sortedKo01pos.bam.bam
87478404 in total
0 QC failure
0 duplicates
87478404 mapped (100.00%)
87478404 paired in sequencing
43739202 read1
43739202 read2
83948534 properly paired (95.96%)
87478404 with itself and mate mapped
0 singletons (0.00%)
0 with mate mapped to a different chr
0 with mate mapped to a different chr (mapQ>=5)
sortedKo01pos.sorted.bam
87478404 in total
0 QC failure
0 duplicates
87478404 mapped (100.00%)
87478404 paired in sequencing
43739202 read1
43739202 read2
83948534 properly paired (95.96%)
87478404 with itself and mate mapped
0 singletons (0.00%)
0 with mate mapped to a different chr
0 with mate mapped to a different chr (mapQ>=5)
sortedKo02pos.bam.bam
110341946 in total
0 QC failure
0 duplicates
110341946 mapped (100.00%)
110341946 paired in sequencing
55170973 read1
55170973 read2
105858916 properly paired (95.94%)
110341946 with itself and mate mapped
0 singletons (0.00%)
0 with mate mapped to a different chr
0 with mate mapped to a different chr (mapQ>=5)
sortedKo02pos.sorted.bam
110341946 in total
0 QC failure
0 duplicates
110341946 mapped (100.00%)
110341946 paired in sequencing
55170973 read1
55170973 read2
105858916 properly paired (95.94%)
110341946 with itself and mate mapped
0 singletons (0.00%)
0 with mate mapped to a different chr
0 with mate mapped to a different chr (mapQ>=5)
sortedKo1IL4pos.bam
108167752 in total
0 QC failure
0 duplicates
108167752 mapped (100.00%)
108167752 paired in sequencing
54083876 read1
54083876 read2
103740354 properly paired (95.91%)
108167752 with itself and mate mapped
0 singletons (0.00%)
0 with mate mapped to a different chr
0 with mate mapped to a different chr (mapQ>=5)
sortedKO21pos.bam
106285524 in total
0 QC failure
0 duplicates
106285524 mapped (100.00%)
106285524 paired in sequencing
53142762 read1
53142762 read2
102128566 properly paired (96.09%)
106285524 with itself and mate mapped
0 singletons (0.00%)
0 with mate mapped to a different chr
0 with mate mapped to a different chr (mapQ>=5)
sortedKO22pos.bam
104574206 in total
0 QC failure
0 duplicates
104574206 mapped (100.00%)
104574206 paired in sequencing
52287103 read1
52287103 read2
100364094 properly paired (95.97%)
104574206 with itself and mate mapped
0 singletons (0.00%)
0 with mate mapped to a different chr
0 with mate mapped to a different chr (mapQ>=5)
sortedKo2IL4pos.bam
111582688 in total
0 QC failure
0 duplicates
111582688 mapped (100.00%)
111582688 paired in sequencing
55791344 read1
55791344 read2
106079606 properly paired (95.07%)
111582688 with itself and mate mapped
0 singletons (0.00%)
0 with mate mapped to a different chr
0 with mate mapped to a different chr (mapQ>=5)
sortedKo61pos.bam
99355884 in total
0 QC failure
0 duplicates
99355884 mapped (100.00%)
99355884 paired in sequencing
49677942 read1
49677942 read2
95376846 properly paired (96.00%)
99355884 with itself and mate mapped
0 singletons (0.00%)
0 with mate mapped to a different chr
0 with mate mapped to a different chr (mapQ>=5)
sortedKo62pos.bam
118684618 in total
0 QC failure
0 duplicates
118684618 mapped (100.00%)
118684618 paired in sequencing
59342309 read1
59342309 read2
113941316 properly paired (96.00%)
118684618 with itself and mate mapped
0 singletons (0.00%)
0 with mate mapped to a different chr
0 with mate mapped to a different chr (mapQ>=5)
sortedKOIFN1pos.bam
109524238 in total
0 QC failure
0 duplicates
109524238 mapped (100.00%)
109524238 paired in sequencing
54762119 read1
54762119 read2
104657546 properly paired (95.56%)
109524238 with itself and mate mapped
0 singletons (0.00%)
0 with mate mapped to a different chr
0 with mate mapped to a different chr (mapQ>=5)
sortedKOIFN2pos.bam
95073216 in total
0 QC failure
0 duplicates
95073216 mapped (100.00%)
95073216 paired in sequencing
47536608 read1
47536608 read2
90983864 properly paired (95.70%)
95073216 with itself and mate mapped
0 singletons (0.00%)
0 with mate mapped to a different chr
0 with mate mapped to a different chr (mapQ>=5)
sortedwt01IL4pos.bam
99134314 in total
0 QC failure
0 duplicates
99134314 mapped (100.00%)
99134314 paired in sequencing
49567157 read1
49567157 read2
94787226 properly paired (95.61%)
99134314 with itself and mate mapped
0 singletons (0.00%)
0 with mate mapped to a different chr
0 with mate mapped to a different chr (mapQ>=5)
sortedwt01pos.bam
78892142 in total
0 QC failure
0 duplicates
78892142 mapped (100.00%)
78892142 paired in sequencing
39446071 read1
39446071 read2
75557584 properly paired (95.77%)
78892142 with itself and mate mapped
0 singletons (0.00%)
0 with mate mapped to a different chr
0 with mate mapped to a different chr (mapQ>=5)
sortedwt01pos.sorted.bam
78892142 in total
0 QC failure
0 duplicates
78892142 mapped (100.00%)
78892142 paired in sequencing
39446071 read1
39446071 read2
75557584 properly paired (95.77%)
78892142 with itself and mate mapped
0 singletons (0.00%)
0 with mate mapped to a different chr
0 with mate mapped to a different chr (mapQ>=5)
sortedwt02IL4pos.bam
76211282 in total
0 QC failure
0 duplicates
76211282 mapped (100.00%)
76211282 paired in sequencing
38105641 read1
38105641 read2
72925806 properly paired (95.69%)
76211282 with itself and mate mapped
0 singletons (0.00%)
0 with mate mapped to a different chr
0 with mate mapped to a different chr (mapQ>=5)
sortedwt02pos.bam
80142586 in total
0 QC failure
0 duplicates
80142586 mapped (100.00%)
80142586 paired in sequencing
40071293 read1
40071293 read2
77054772 properly paired (96.15%)
80142586 with itself and mate mapped
0 singletons (0.00%)
0 with mate mapped to a different chr
0 with mate mapped to a different chr (mapQ>=5)
sortedwt02pos.sorted.bam
80142586 in total
0 QC failure
0 duplicates
80142586 mapped (100.00%)
80142586 paired in sequencing
40071293 read1
40071293 read2
77054772 properly paired (96.15%)
80142586 with itself and mate mapped
0 singletons (0.00%)
0 with mate mapped to a different chr
0 with mate mapped to a different chr (mapQ>=5)
sortedwt21pos.bam
74306938 in total
0 QC failure
0 duplicates
74306938 mapped (100.00%)
74306938 paired in sequencing
37153469 read1
37153469 read2
71484492 properly paired (96.20%)
74306938 with itself and mate mapped
0 singletons (0.00%)
0 with mate mapped to a different chr
0 with mate mapped to a different chr (mapQ>=5)
sortedwt22pos.bam
87248728 in total
0 QC failure
0 duplicates
87248728 mapped (100.00%)
87248728 paired in sequencing
43624364 read1
43624364 read2
84157528 properly paired (96.46%)
87248728 with itself and mate mapped
0 singletons (0.00%)
0 with mate mapped to a different chr
0 with mate mapped to a different chr (mapQ>=5)
sortedwt61pos.bam
84787966 in total
0 QC failure
0 duplicates
84787966 mapped (100.00%)
84787966 paired in sequencing
42393983 read1
42393983 read2
81587466 properly paired (96.23%)
84787966 with itself and mate mapped
0 singletons (0.00%)
0 with mate mapped to a different chr
0 with mate mapped to a different chr (mapQ>=5)
sortedwt62pos.bam
82890936 in total
0 QC failure
0 duplicates
82890936 mapped (100.00%)
82890936 paired in sequencing
41445468 read1
41445468 read2
79545294 properly paired (95.96%)
82890936 with itself and mate mapped
0 singletons (0.00%)
0 with mate mapped to a different chr
0 with mate mapped to a different chr (mapQ>=5)
sortedwtIFN1pos.bam
84938076 in total
0 QC failure
0 duplicates
84938076 mapped (100.00%)
84938076 paired in sequencing
42469038 read1
42469038 read2
81212512 properly paired (95.61%)
84938076 with itself and mate mapped
0 singletons (0.00%)
0 with mate mapped to a different chr
0 with mate mapped to a different chr (mapQ>=5)
sortedwtIFN2pos.bam
112692222 in total
0 QC failure
0 duplicates
112692222 mapped (100.00%)
112692222 paired in sequencing
56346111 read1
56346111 read2
107873494 properly paired (95.72%)
112692222 with itself and mate mapped
0 singletons (0.00%)
0 with mate mapped to a different chr
0 with mate mapped to a different chr (mapQ>=5)