BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238303.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 = 1,510,113 number of mapped reads = 1,367,303 (90.54%) number of supplementary alignments = 13,111 (0.87%) number of secondary alignments = 0 number of mapped bases = 91,055,616 bp number of sequenced bases = 91,018,722 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 35,861 duplication rate = 1.7% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.451 >>>>>>> ACTG content number of A's = 26,172,475 bp (28.76%) number of C's = 17,481,277 bp (19.21%) number of T's = 27,398,629 bp (30.1%) number of G's = 19,936,918 bp (21.9%) number of N's = 29,423 bp (0.03%) GC percentage = 41.11% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 752,479 number of insertions = 7,138 mapped reads with insertion percentage = 0.52% number of deletions = 21,438 mapped reads with deletion percentage = 1.55% homopolymer indels = 45.87% >>>>>>> Coverage mean coverageData = 0.0294X std coverageData = 0.3335X There is a 2.69% of reference with a coverageData >= 1X There is a 0.16% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 7602338 0.03050077857178137 0.7309811056668122 chr2 243199373 7012294 0.028833520060103115 0.35057667603499904 chr3 198022430 7019084 0.03544590377968799 0.20107197487114914 chr4 191154276 5684532 0.029737927494752982 0.19117673112195602 chr5 180915260 5076450 0.02805982204044037 0.17874361566342323 chr6 171115067 4923886 0.028775291891742064 0.2127575866144015 chr7 159138663 3771816 0.023701443312993023 0.3459972239785242 chr8 146364022 4757481 0.032504442929287634 0.46094186713763224 chr9 141213431 3542556 0.025086537271373287 0.2602299946749757 chr10 135534747 4167882 0.030751391006765223 0.2737755222531405 chr11 135006516 4696362 0.0347861876533426 0.29904383353607095 chr12 133851895 4240291 0.0316789762296604 0.19090293133073377 chr13 115169878 3360138 0.02917549326569574 0.18017083435126022 chr14 107349540 3544040 0.03301402129902001 0.20407920738572471 chr15 102531392 2588185 0.025242854403069063 0.17347320964181573 chr16 90354753 2321838 0.025696910487929728 0.18599319391591881 chr17 81195210 2312352 0.028478921355089788 0.2017361851273332 chr18 78077248 2184024 0.027972604772135413 0.5078191062568177 chr19 59128983 1762707 0.029811217960572737 0.49422499903912703 chr20 63025520 2048016 0.032495027411118545 0.1987730462431661 chr21 48129895 1229800 0.025551686742719883 0.178447634217371 chr22 51304566 837765 0.016329248355789618 0.13396160022283116 chrMT 16571 10033 0.605455313499487 0.8117282592710445 chrX 155270560 6118396 0.039404739700816434 0.22761475962650568 chrY 59373566 243350 0.00409862530406208 0.09033298251076126