BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080920.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 4,935,006 number of mapped reads = 4,489,595 (90.97%) number of supplementary alignments = 50,589 (1.03%) number of secondary alignments = 0 number of mapped bases = 308,948,922 bp number of sequenced bases = 308,836,237 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 241,710 duplication rate = 4.22% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.9043 >>>>>>> ACTG content number of A's = 89,548,844 bp (29%) number of C's = 54,627,691 bp (17.69%) number of T's = 99,309,072 bp (32.16%) number of G's = 63,861,402 bp (20.68%) number of N's = 1,489,228 bp (0.48%) GC percentage = 38.37% >>>>>>> Mismatches and indels general error rate = 0.0118 number of mismatches = 3,607,298 number of insertions = 23,612 mapped reads with insertion percentage = 0.52% number of deletions = 68,995 mapped reads with deletion percentage = 1.52% homopolymer indels = 50.26% >>>>>>> Coverage mean coverageData = 0.0998X std coverageData = 0.6819X There is a 6.92% of reference with a coverageData >= 1X There is a 1.98% of reference with a coverageData >= 2X There is a 0.62% of reference with a coverageData >= 3X There is a 0.21% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 24287576 0.09744238912046682 1.0914713540002974 chr2 243199373 26681412 0.10971003613566059 0.637677515232079 chr3 198022430 21976918 0.110981963002878 0.44883570501264647 chr4 191154276 21883755 0.11448216308799705 0.46901219503604197 chr5 180915260 20291612 0.11216086470538748 0.4529198728515649 chr6 171115067 18719691 0.109398262398483 0.6065601781601931 chr7 159138663 17296937 0.1086909785084722 1.0141779398828517 chr8 146364022 16026647 0.10949854192992865 1.3324155696043822 chr9 141213431 12744889 0.0902526686714382 0.5837742876229143 chr10 135534747 13929842 0.10277690635302547 0.5894889743344011 chr11 135006516 13936904 0.10323134329308965 0.5417070914114488 chr12 133851895 14124091 0.10552029166266193 0.44183487249814646 chr13 115169878 10682330 0.09275281163361135 0.41072307136979636 chr14 107349540 9692002 0.09028452287732207 0.43272538405822275 chr15 102531392 8465831 0.08256818555628309 0.38674952888443365 chr16 90354753 7578881 0.08387916239447857 0.42045796423884124 chr17 81195210 6757212 0.08322180581834815 0.43670981431401973 chr18 78077248 8618489 0.11038412880535953 1.08414209360578 chr19 59128983 4358516 0.07371200685119174 0.7472917348733736 chr20 63025520 5636284 0.08942859971643233 0.42364078410087275 chr21 48129895 4122423 0.08565202562773096 0.4226038687532829 chr22 51304566 2587082 0.05042596013773901 0.2948094554120279 chrMT 16571 14537 0.8772554462615413 1.3209547206479417 chrX 155270560 17903431 0.11530473645486948 0.5000117930622726 chrY 59373566 631630 0.010638235877562078 0.18198723951752674