BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089733.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 25,414,726 number of mapped reads = 21,868,887 (86.05%) number of supplementary alignments = 1,237 (0%) number of secondary alignments = 0 number of mapped bases = 1,034,181,078 bp number of sequenced bases = 1,033,969,985 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,006,582 duplication rate = 11.9% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1314 >>>>>>> ACTG content number of A's = 313,881,150 bp (30.36%) number of C's = 205,353,610 bp (19.86%) number of T's = 298,180,584 bp (28.84%) number of G's = 216,532,092 bp (20.94%) number of N's = 22,549 bp (0%) GC percentage = 40.8% >>>>>>> Mismatches and indels general error rate = 0.0039 number of mismatches = 4,001,132 number of insertions = 43,821 mapped reads with insertion percentage = 0.2% number of deletions = 140,114 mapped reads with deletion percentage = 0.64% homopolymer indels = 49.15% >>>>>>> Coverage mean coverageData = 0.3341X std coverageData = 2.249X There is a 11.69% of reference with a coverageData >= 1X There is a 7.05% of reference with a coverageData >= 2X There is a 4.58% of reference with a coverageData >= 3X There is a 3.02% of reference with a coverageData >= 4X There is a 2.01% of reference with a coverageData >= 5X There is a 1.35% of reference with a coverageData >= 6X There is a 0.91% of reference with a coverageData >= 7X There is a 0.62% of reference with a coverageData >= 8X There is a 0.43% of reference with a coverageData >= 9X There is a 0.31% of reference with a coverageData >= 10X There is a 0.22% of reference with a coverageData >= 11X There is a 0.16% of reference with a coverageData >= 12X There is a 0.12% of reference with a coverageData >= 13X There is a 0.09% of reference with a coverageData >= 14X There is a 0.07% of reference with a coverageData >= 15X There is a 0.05% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% 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 82220998 0.32987279096889394 3.8197150717734707 chr2 243199373 88904706 0.3655630559540957 2.2466746521627323 chr3 198022430 70086076 0.3539299866181826 1.3178610437093055 chr4 191154276 66770180 0.34929995497458816 1.4468625971600022 chr5 180915260 64360436 0.3557490727979497 1.3429123210133806 chr6 171115067 59870810 0.349886255194582 1.5538057910376326 chr7 159138663 56817059 0.357028631062459 3.321381363970696 chr8 146364022 53199923 0.3634767771003177 3.835665925990066 chr9 141213431 43431136 0.3075566940937792 1.9780760307839698 chr10 135534747 47710868 0.3520194566785151 1.9586514973756872 chr11 135006516 47121851 0.3490339014451717 2.055472478322287 chr12 133851895 46742633 0.3492115894212779 1.4468997056361745 chr13 115169878 33213542 0.2883874028242003 1.1881246717408787 chr14 107349540 31992745 0.298024053014107 1.4408629717769574 chr15 102531392 29212948 0.28491711104439116 1.1899377517016645 chr16 90354753 28063269 0.3105898479961536 1.3480141993483636 chr17 81195210 27130469 0.33413878725111984 1.5726088886432787 chr18 78077248 27048556 0.3464332656806756 3.7779104875774725 chr19 59128983 19861127 0.33589495357970217 3.1612049745526587 chr20 63025520 21324079 0.33834038973419023 1.393132147485957 chr21 48129895 13380363 0.278005239778728 1.4303916877285763 chr22 51304566 11329608 0.2208304032822342 0.9995739054600514 chrMT 16571 980649 59.17862530927524 33.98141113735148 chrX 155270560 60229188 0.38789831118017476 1.6825743558314756 chrY 59373566 3177859 0.05352312845753614 1.1723823491382517