BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR9716726.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.result/quality.files/genome_results.txt
>>>>>>> Reference
number of bases = 3,095,693,983 bp
number of contigs = 25
>>>>>>> Globals
number of windows = 424
number of reads = 1,131,721
number of mapped reads = 991,750 (87.63%)
number of supplementary alignments = 4,699 (0.42%)
number of secondary alignments = 0
number of mapped bases = 57,887,941 bp
number of sequenced bases = 57,870,858 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 24,903
duplication rate = 1.68%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.3475
>>>>>>> ACTG content
number of A's = 15,399,066 bp (26.61%)
number of C's = 10,658,102 bp (18.42%)
number of T's = 17,783,915 bp (30.73%)
number of G's = 14,029,077 bp (24.24%)
number of N's = 698 bp (0%)
GC percentage = 42.66%
>>>>>>> Mismatches and indels
general error rate = 0.0051
number of mismatches = 289,087
number of insertions = 4,225
mapped reads with insertion percentage = 0.42%
number of deletions = 10,817
mapped reads with deletion percentage = 1.08%
homopolymer indels = 41.21%
>>>>>>> Coverage
mean coverageData = 0.0187X
std coverageData = 0.2056X
There is a 1.72% of reference with a coverageData >= 1X
There is a 0.1% of reference with a coverageData >= 2X
There is a 0.01% of reference with a coverageData >= 3X
There is a 0.01% of reference with a coverageData >= 4X
There is a 0% of reference with a coverageData >= 5X
There is a 0% of reference with a coverageData >= 6X
There is a 0% of reference with a coverageData >= 7X
There is a 0% of reference with a coverageData >= 8X
There is a 0% of reference with a coverageData >= 9X
There is a 0% of reference with a coverageData >= 10X
There is a 0% of reference with a coverageData >= 11X
There is a 0% of reference with a coverageData >= 12X
There is a 0% of reference with a coverageData >= 13X
There is a 0% of reference with a coverageData >= 14X
There is a 0% of reference with a coverageData >= 15X
There is a 0% of reference with a coverageData >= 16X
There is a 0% of reference with a coverageData >= 17X
There is a 0% of reference with a coverageData >= 18X
There is a 0% of reference with a coverageData >= 19X
There is a 0% of reference with a coverageData >= 20X
There is a 0% of reference with a coverageData >= 21X
There is a 0% of reference with a coverageData >= 22X
There is a 0% of reference with a coverageData >= 23X
There is a 0% of reference with a coverageData >= 24X
There is a 0% of reference with a coverageData >= 25X
There is a 0% of reference with a coverageData >= 26X
There is a 0% of reference with a coverageData >= 27X
There is a 0% of reference with a coverageData >= 28X
There is a 0% of reference with a coverageData >= 29X
There is a 0% of reference with a coverageData >= 30X
There is a 0% of reference with a coverageData >= 31X
There is a 0% of reference with a coverageData >= 32X
There is a 0% of reference with a coverageData >= 33X
There is a 0% of reference with a coverageData >= 34X
There is a 0% of reference with a coverageData >= 35X
There is a 0% of reference with a coverageData >= 36X
There is a 0% of reference with a coverageData >= 37X
There is a 0% of reference with a coverageData >= 38X
There is a 0% of reference with a coverageData >= 39X
There is a 0% of reference with a coverageData >= 40X
There is a 0% of reference with a coverageData >= 41X
There is a 0% of reference with a coverageData >= 42X
There is a 0% of reference with a coverageData >= 43X
There is a 0% of reference with a coverageData >= 44X
There is a 0% of reference with a coverageData >= 45X
There is a 0% of reference with a coverageData >= 46X
There is a 0% of reference with a coverageData >= 47X
There is a 0% of reference with a coverageData >= 48X
There is a 0% of reference with a coverageData >= 49X
There is a 0% of reference with a coverageData >= 50X
There is a 0% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 3961301 0.015892843051331856 0.24721055093340835
chr2 243199373 5507545 0.022646213812401565 0.23134748780829226
chr3 198022430 4879216 0.02463971379403838 0.18342263957679059
chr4 191154276 4037037 0.02111926075878104 0.15929111198585194
chr5 180915260 3055732 0.01689040493322675 0.1382992589936308
chr6 171115067 3145953 0.018385014570341723 0.14995166035157506
chr7 159138663 2841622 0.01785626413111187 0.4290874420544113
chr8 146364022 4640201 0.03170315311504626 0.22433743604806392
chr9 141213431 2368760 0.016774325099430522 0.14972320436410622
chr10 135534747 2668423 0.01968810994275881 0.30562367138730917
chr11 135006516 2089001 0.015473334635196423 0.1493206220399213
chr12 133851895 2693720 0.020124631033426908 0.17042680012417316
chr13 115169878 1464488 0.012715894341747936 0.11881632617020697
chr14 107349540 1800301 0.01677045844816848 0.13880028701473926
chr15 102531392 1328042 0.012952540427813563 0.1256651409653184
chr16 90354753 1680930 0.01860366991429881 0.15218713318266158
chr17 81195210 2329476 0.028689820495568643 0.18445122850763127
chr18 78077248 1428680 0.01829828838229544 0.21587165288228233
chr19 59128983 1122785 0.018988741950795942 0.25921735937856005
chr20 63025520 1265314 0.020076216745216858 0.1651342959170306
chr21 48129895 584717 0.012148727937179169 0.12124112868122029
chr22 51304566 840416 0.016380920169951345 0.13477151765715745
chrMT 16571 18988 1.1458572204453563 1.3143128135762825
chrX 155270560 2004038 0.01290674806608542 0.13661259852595053
chrY 59373566 131255 0.0022106639173399153 0.06370404313033919