BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080746.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 = 6,354,729 number of mapped reads = 4,710,757 (74.13%) number of supplementary alignments = 26,388 (0.42%) number of secondary alignments = 0 number of mapped bases = 300,034,387 bp number of sequenced bases = 299,936,617 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 480,498 duplication rate = 7.91% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6447 >>>>>>> ACTG content number of A's = 93,045,506 bp (31.02%) number of C's = 60,900,880 bp (20.3%) number of T's = 76,574,161 bp (25.53%) number of G's = 68,737,193 bp (22.92%) number of N's = 678,877 bp (0.23%) GC percentage = 43.22% >>>>>>> Mismatches and indels general error rate = 0.0101 number of mismatches = 3,000,884 number of insertions = 21,765 mapped reads with insertion percentage = 0.46% number of deletions = 51,797 mapped reads with deletion percentage = 1.09% homopolymer indels = 42.7% >>>>>>> Coverage mean coverageData = 0.0969X std coverageData = 0.6066X There is a 6.46% of reference with a coverageData >= 1X There is a 1.85% of reference with a coverageData >= 2X There is a 0.67% 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 0.02% 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% 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 37539956 0.15061128373276952 0.8964290832542415 chr2 243199373 21727130 0.08933875828701253 0.5858426232698202 chr3 198022430 18125189 0.09153098969647025 0.4316261415421248 chr4 191154276 17846106 0.09335970072675748 0.5432359900074593 chr5 180915260 16174924 0.08940607884597462 0.42294508205185644 chr6 171115067 19973492 0.11672550144283905 0.6325570924819284 chr7 159138663 20763047 0.13047141787285219 0.9351093290191388 chr8 146364022 13740978 0.0938822110258763 0.7600515683930132 chr9 141213431 10688937 0.07569348697433745 0.46871295503000154 chr10 135534747 13431632 0.09910102241161818 0.7071459966249 chr11 135006516 12364481 0.09158432767793223 0.5554613142861603 chr12 133851895 11865226 0.08864443794389314 0.4355870761730958 chr13 115169878 12069380 0.10479632530304495 0.46729697985995966 chr14 107349540 8350440 0.07778738502279563 0.4588966553358901 chr15 102531392 7549834 0.07363436556093962 0.3887874805389953 chr16 90354753 9402164 0.10405832220027207 0.5263741127102572 chr17 81195210 7091019 0.0873329719819679 0.44528648190649717 chr18 78077248 4331712 0.05547982428888887 0.7341321747348493 chr19 59128983 5576635 0.09431305456412128 0.7949174034121288 chr20 63025520 5938475 0.09422334000576274 0.458557700289911 chr21 48129895 5095540 0.10587058209871432 0.5920220603155423 chr22 51304566 3377343 0.06582928700732017 0.3743009695883863 chrMT 16571 35247 2.127029147305534 2.3420653967840885 chrX 155270560 16049047 0.10336181565906634 0.487640730201634 chrY 59373566 926453 0.015603795803674651 0.4432192681829397