BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524888.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,768,006 number of mapped reads = 1,620,801 (91.67%) number of supplementary alignments = 6,228 (0.35%) number of secondary alignments = 0 number of mapped bases = 94,672,164 bp number of sequenced bases = 94,643,730 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 63,059 duplication rate = 2.84% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1907 >>>>>>> ACTG content number of A's = 24,562,314 bp (25.95%) number of C's = 17,438,353 bp (18.43%) number of T's = 30,544,956 bp (32.27%) number of G's = 22,085,009 bp (23.33%) number of N's = 13,098 bp (0.01%) GC percentage = 41.76% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 470,261 number of insertions = 6,577 mapped reads with insertion percentage = 0.4% number of deletions = 17,817 mapped reads with deletion percentage = 1.09% homopolymer indels = 42.63% >>>>>>> Coverage mean coverageData = 0.0306X std coverageData = 0.3035X There is a 2.76% of reference with a coverageData >= 1X There is a 0.21% of reference with a coverageData >= 2X There is a 0.03% 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 7587239 0.03044020098950927 0.5840643586753252 chr2 243199373 7972258 0.03278075063129377 0.32870708466488924 chr3 198022430 6300215 0.03181566350842175 0.1919886094826793 chr4 191154276 6053206 0.031666600018929215 0.21398840875806857 chr5 180915260 5761118 0.031844289973106746 0.19463684224168035 chr6 171115067 5453331 0.03186937945096325 0.21159724158566534 chr7 159138663 5219545 0.03279872346294627 0.439826997831651 chr8 146364022 4885112 0.03337645367520715 0.28624012383354436 chr9 141213431 4038154 0.028596104289824953 0.2737738618826702 chr10 135534747 4563572 0.03367086375274674 0.2818398308318111 chr11 135006516 4312637 0.0319439174328445 0.27016533791667174 chr12 133851895 4327628 0.032331466058063654 0.20083302388371344 chr13 115169878 3002517 0.02607033238326431 0.17434305083648166 chr14 107349540 2892112 0.02694107492216548 0.1877720572781233 chr15 102531392 2691130 0.026246888367613307 0.17525012609586696 chr16 90354753 2725125 0.030160283875713765 0.21020303860247838 chr17 81195210 2509724 0.03090975440546308 0.20740037840244527 chr18 78077248 2553574 0.03270573778420059 0.5244970402523514 chr19 59128983 1811772 0.030641014069191754 0.3991810733814384 chr20 63025520 1985045 0.03149589245753149 0.19561935818520113 chr21 48129895 1251921 0.026011297136634103 0.19575479327162312 chr22 51304566 1117035 0.02177262351269086 0.1594974521639782 chrMT 16571 16461 0.9933618972904472 1.2388949564061151 chrX 155270560 5352102 0.03446952210386824 0.231942519829104 chrY 59373566 289631 0.004878113603619496 0.1301805545586945