BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472591.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 = 5,533,068 number of mapped reads = 5,112,468 (92.4%) number of supplementary alignments = 169,123 (3.06%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,583,007 number of mapped paired reads (second in pair) = 2,529,461 number of mapped paired reads (both in pair) = 4,982,604 number of mapped paired reads (singletons) = 129,864 number of mapped bases = 416,735,689 bp number of sequenced bases = 416,555,761 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 649,077 duplication rate = 11.22% >>>>>>> Insert size mean insert size = 274,322.2771 std insert size = 5,060,131.5676 median insert size = 133 >>>>>>> Mapping quality mean mapping quality = 50.3883 >>>>>>> ACTG content number of A's = 106,669,776 bp (25.61%) number of C's = 83,266,805 bp (19.99%) number of T's = 124,140,012 bp (29.8%) number of G's = 102,221,234 bp (24.54%) number of N's = 257,934 bp (0.06%) GC percentage = 44.53% >>>>>>> Mismatches and indels general error rate = 0.0119 number of mismatches = 4,886,687 number of insertions = 39,611 mapped reads with insertion percentage = 0.76% number of deletions = 95,275 mapped reads with deletion percentage = 1.83% homopolymer indels = 42.47% >>>>>>> Coverage mean coverageData = 0.1346X std coverageData = 1.1708X There is a 8.44% of reference with a coverageData >= 1X There is a 3.19% of reference with a coverageData >= 2X There is a 0.86% of reference with a coverageData >= 3X There is a 0.35% of reference with a coverageData >= 4X There is a 0.14% of reference with a coverageData >= 5X There is a 0.07% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% 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 26110780 0.1047571311768166 1.4332152866036871 chr2 243199373 39310767 0.16164008366913019 1.7794271544147544 chr3 198022430 20467178 0.10335787718593292 0.4389458416605422 chr4 191154276 19466972 0.10183906113614744 0.6658765497193498 chr5 180915260 18268431 0.10097783348955748 0.4471320975524166 chr6 171115067 25315973 0.1479470711950807 0.721331098504018 chr7 159138663 37462105 0.23540542752957527 2.009373780279849 chr8 146364022 19094359 0.13045800968765398 1.0637299787730092 chr9 141213431 13374764 0.09471311549678302 1.2758407847805215 chr10 135534747 21857430 0.1612680916429497 1.1661158274030219 chr11 135006516 20736897 0.15359923072157494 1.2070185677094845 chr12 133851895 20217788 0.151045960163657 0.5509310696789649 chr13 115169878 18247833 0.15844275705493063 0.5702903547927625 chr14 107349540 9932290 0.09252289297187487 2.161910820977973 chr15 102531392 11794754 0.11503553955455906 0.4790094175894459 chr16 90354753 14692833 0.16261272940450625 0.7525715756355493 chr17 81195210 12763082 0.15719008547425395 0.9584783412192973 chr18 78077248 8352803 0.10698126808977694 2.0314873285726134 chr19 59128983 7110572 0.12025527312045939 1.0543628324158252 chr20 63025520 16057997 0.254785632867448 0.8435563782941992 chr21 48129895 5965771 0.1239514650925376 0.5982265898151736 chr22 51304566 3989183 0.07775493120826711 0.3864600041870634 chrMT 16571 228129 13.76676120934162 8.927604298793817 chrX 155270560 24906125 0.16040468328316715 0.7263062062348645 chrY 59373566 1010873 0.017025640669788976 0.5172868290181499