BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472504.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 14,344,428 number of mapped reads = 14,123,617 (98.46%) number of supplementary alignments = 57,225 (0.4%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,097,043 number of mapped paired reads (second in pair) = 7,026,574 number of mapped paired reads (both in pair) = 14,008,934 number of mapped paired reads (singletons) = 114,683 number of mapped bases = 1,390,558,509 bp number of sequenced bases = 1,390,390,584 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,501,693 duplication rate = 44.21% >>>>>>> Insert size mean insert size = 32,169.2196 std insert size = 1,754,324.8005 median insert size = 243 >>>>>>> Mapping quality mean mapping quality = 55.2086 >>>>>>> ACTG content number of A's = 387,413,581 bp (27.86%) number of C's = 310,822,181 bp (22.36%) number of T's = 384,172,325 bp (27.63%) number of G's = 307,779,465 bp (22.14%) number of N's = 203,032 bp (0.01%) GC percentage = 44.49% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 10,302,695 number of insertions = 72,580 mapped reads with insertion percentage = 0.51% number of deletions = 73,865 mapped reads with deletion percentage = 0.52% homopolymer indels = 44.03% >>>>>>> Coverage mean coverageData = 0.4492X std coverageData = 17.5464X There is a 4.65% of reference with a coverageData >= 1X There is a 1.99% of reference with a coverageData >= 2X There is a 0.88% of reference with a coverageData >= 3X There is a 0.63% of reference with a coverageData >= 4X There is a 0.47% of reference with a coverageData >= 5X There is a 0.42% of reference with a coverageData >= 6X There is a 0.38% of reference with a coverageData >= 7X There is a 0.35% of reference with a coverageData >= 8X There is a 0.34% of reference with a coverageData >= 9X There is a 0.32% of reference with a coverageData >= 10X There is a 0.31% of reference with a coverageData >= 11X There is a 0.3% of reference with a coverageData >= 12X There is a 0.29% of reference with a coverageData >= 13X There is a 0.28% of reference with a coverageData >= 14X There is a 0.27% of reference with a coverageData >= 15X There is a 0.26% of reference with a coverageData >= 16X There is a 0.26% of reference with a coverageData >= 17X There is a 0.25% of reference with a coverageData >= 18X There is a 0.24% of reference with a coverageData >= 19X There is a 0.24% of reference with a coverageData >= 20X There is a 0.23% of reference with a coverageData >= 21X There is a 0.23% of reference with a coverageData >= 22X There is a 0.22% of reference with a coverageData >= 23X There is a 0.22% of reference with a coverageData >= 24X There is a 0.21% of reference with a coverageData >= 25X There is a 0.21% of reference with a coverageData >= 26X There is a 0.2% of reference with a coverageData >= 27X There is a 0.2% of reference with a coverageData >= 28X There is a 0.2% of reference with a coverageData >= 29X There is a 0.19% of reference with a coverageData >= 30X There is a 0.19% of reference with a coverageData >= 31X There is a 0.19% of reference with a coverageData >= 32X There is a 0.18% of reference with a coverageData >= 33X There is a 0.18% of reference with a coverageData >= 34X There is a 0.18% of reference with a coverageData >= 35X There is a 0.17% of reference with a coverageData >= 36X There is a 0.17% of reference with a coverageData >= 37X There is a 0.17% of reference with a coverageData >= 38X There is a 0.17% of reference with a coverageData >= 39X There is a 0.16% of reference with a coverageData >= 40X There is a 0.16% of reference with a coverageData >= 41X There is a 0.16% of reference with a coverageData >= 42X There is a 0.16% of reference with a coverageData >= 43X There is a 0.15% of reference with a coverageData >= 44X There is a 0.15% of reference with a coverageData >= 45X There is a 0.15% of reference with a coverageData >= 46X There is a 0.15% of reference with a coverageData >= 47X There is a 0.15% of reference with a coverageData >= 48X There is a 0.14% of reference with a coverageData >= 49X There is a 0.14% of reference with a coverageData >= 50X There is a 0.14% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 152406742 0.6114598286196447 20.51621329683704 chr2 243199373 119482319 0.49129369671524603 37.149895411781245 chr3 198022430 159816829 0.8070642754964678 19.49305748971252 chr4 191154276 54432466 0.2847567270742089 10.650215723572387 chr5 180915260 78087838 0.4316265968940376 15.725285683922067 chr6 171115067 75250450 0.439765190285669 11.876358367970099 chr7 159138663 70844457 0.4451743885770864 16.35588314208886 chr8 146364022 55052977 0.37613736113373547 13.762814494229719 chr9 141213431 76872485 0.5443709175227107 13.978066882156616 chr10 135534747 35501905 0.26193950839779856 9.151432545902406 chr11 135006516 52895302 0.3917981410615766 11.54300887835548 chr12 133851895 96513587 0.721047595179732 20.903620654758296 chr13 115169878 23367283 0.20289405012654438 7.714919900278947 chr14 107349540 32554645 0.30325835583459415 11.999881325054 chr15 102531392 36079554 0.3518878783972815 11.594029904148165 chr16 90354753 30469703 0.33722302356357503 7.929979187527365 chr17 81195210 55748360 0.6865966600739132 15.984517091081997 chr18 78077248 26487368 0.3392456660357701 14.464943962933724 chr19 59128983 30682106 0.5189012975244306 15.55338645500559 chr20 63025520 42539308 0.6749537012943329 20.531774149390625 chr21 48129895 5675169 0.11791359611318496 5.005420585274847 chr22 51304566 10155472 0.19794479890932123 6.602206898808039 chrMT 16571 1799 0.10856315249532315 0.45995219849740443 chrX 155270560 67747007 0.4363158540807736 15.443145996425079 chrY 59373566 1893378 0.03188924175448717 3.4948938911394714