BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080752.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 = 6,344,035 number of mapped reads = 4,708,278 (74.22%) number of supplementary alignments = 29,551 (0.47%) number of secondary alignments = 0 number of mapped bases = 294,577,273 bp number of sequenced bases = 294,479,470 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 479,715 duplication rate = 8.16% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.7785 >>>>>>> ACTG content number of A's = 88,823,276 bp (30.16%) number of C's = 60,456,030 bp (20.53%) number of T's = 78,804,169 bp (26.76%) number of G's = 65,746,771 bp (22.33%) number of N's = 649,224 bp (0.22%) GC percentage = 42.86% >>>>>>> Mismatches and indels general error rate = 0.0108 number of mismatches = 3,138,748 number of insertions = 22,497 mapped reads with insertion percentage = 0.47% number of deletions = 52,556 mapped reads with deletion percentage = 1.1% homopolymer indels = 42.28% >>>>>>> Coverage mean coverageData = 0.0952X std coverageData = 0.6624X There is a 6.28% of reference with a coverageData >= 1X There is a 1.86% of reference with a coverageData >= 2X There is a 0.68% of reference with a coverageData >= 3X There is a 0.28% of reference with a coverageData >= 4X There is a 0.13% 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 0.01% 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% 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 37037581 0.14859574211452015 0.9574678163736919 chr2 243199373 22309334 0.09173269537993423 0.6207541578737478 chr3 198022430 17743705 0.0896045210635987 0.4260821445110092 chr4 191154276 17278212 0.09038883336305802 0.5540646205514427 chr5 180915260 15900370 0.08788849542045264 0.4183854799552063 chr6 171115067 20078387 0.11733850999807048 0.9447490454143411 chr7 159138663 20291257 0.1275067706205374 1.0271937834030813 chr8 146364022 13507172 0.09228478293661539 0.6936212165252902 chr9 141213431 10520593 0.07450136240935892 0.508861270890482 chr10 135534747 12928143 0.09538618904862825 0.8525612803752131 chr11 135006516 11995262 0.08884950412319358 0.6044958867291581 chr12 133851895 11722198 0.08757588377811162 0.4353448149849076 chr13 115169878 11632869 0.10100617628508732 0.4559918017575691 chr14 107349540 8091352 0.07537388609210621 0.4593721608855343 chr15 102531392 7752652 0.07561247193444912 0.3921877737426026 chr16 90354753 9035181 0.09999674283875248 0.5182692584056129 chr17 81195210 6842038 0.08426652261876039 0.44645590243156474 chr18 78077248 4234452 0.054234134891639627 0.9366149759835264 chr19 59128983 5737522 0.09703400445767857 0.8968977246957422 chr20 63025520 5747637 0.09119539196185926 0.46989167838913426 chr21 48129895 4738853 0.09845965797349028 0.5902541628994615 chr22 51304566 3208695 0.06254209420658582 0.3640105672839406 chrMT 16571 43604 2.631343914066743 2.6616114347046542 chrX 155270560 15244091 0.09817760044144878 0.4902110906429485 chrY 59373566 956113 0.01610334471067478 0.47210784461989935