BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004136.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,712,821 number of mapped reads = 1,410,996 (82.38%) number of supplementary alignments = 12,102 (0.71%) number of secondary alignments = 0 number of mapped bases = 90,813,671 bp number of sequenced bases = 90,771,509 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 66,444 duplication rate = 3.68% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.505 >>>>>>> ACTG content number of A's = 24,634,786 bp (27.14%) number of C's = 16,341,683 bp (18%) number of T's = 29,036,188 bp (31.99%) number of G's = 20,743,599 bp (22.85%) number of N's = 15,253 bp (0.02%) GC percentage = 40.86% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 876,719 number of insertions = 7,589 mapped reads with insertion percentage = 0.53% number of deletions = 25,457 mapped reads with deletion percentage = 1.78% homopolymer indels = 44.93% >>>>>>> Coverage mean coverageData = 0.0293X std coverageData = 0.2948X There is a 2.48% of reference with a coverageData >= 1X There is a 0.33% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% 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 5647450 0.022657716868837812 0.3530001617313807 chr2 243199373 5017910 0.02063290681263393 0.3309766857303066 chr3 198022430 6658650 0.033625736236041544 0.2086118436779866 chr4 191154276 7962557 0.041655134097026425 0.2544328546516074 chr5 180915260 2629098 0.014532206957002964 0.14181602619785214 chr6 171115067 4191279 0.024493921391504348 0.18640427250317673 chr7 159138663 7110870 0.04468348461618029 0.4115966920779304 chr8 146364022 7421887 0.050708411114857174 0.42322322917876803 chr9 141213431 5237376 0.03708837015651861 0.3725549951887053 chr10 135534747 2361400 0.01742283844009389 0.2235462832671844 chr11 135006516 5579476 0.04132745711325519 0.3071488358682912 chr12 133851895 4389929 0.03279691333469728 0.21358685030960675 chr13 115169878 1492135 0.012955948429501679 0.13198693962591784 chr14 107349540 3855335 0.03591384741844259 0.24682580633658724 chr15 102531392 2284891 0.02228479449493868 0.17306077742309386 chr16 90354753 3269745 0.03618785831886453 0.26341562162171417 chr17 81195210 2360448 0.0290712715688524 0.21242115241411905 chr18 78077248 1805688 0.023126942179109593 0.6994592833140009 chr19 59128983 1407574 0.023805144762932925 0.29419396319388263 chr20 63025520 3820098 0.06061192355096792 0.2987165131866536 chr21 48129895 1002627 0.020831688911849902 0.20758710376643447 chr22 51304566 1068457 0.020825768217199225 0.1651787639034883 chrMT 16571 38826 2.3430088709190753 2.1475861728533445 chrX 155270560 3861951 0.024872396930879878 0.20495127600765967 chrY 59373566 338014 0.00569300486347746 0.14771226089706435