BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524401.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 = 1,366,714 number of mapped reads = 1,255,655 (91.87%) number of supplementary alignments = 4,763 (0.35%) number of secondary alignments = 0 number of mapped bases = 73,225,105 bp number of sequenced bases = 73,203,924 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 41,800 duplication rate = 2.45% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8556 >>>>>>> ACTG content number of A's = 18,810,701 bp (25.7%) number of C's = 13,578,244 bp (18.55%) number of T's = 23,506,767 bp (32.11%) number of G's = 17,299,519 bp (23.63%) number of N's = 8,693 bp (0.01%) GC percentage = 42.18% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 361,038 number of insertions = 4,874 mapped reads with insertion percentage = 0.39% number of deletions = 13,272 mapped reads with deletion percentage = 1.05% homopolymer indels = 42.31% >>>>>>> Coverage mean coverageData = 0.0237X std coverageData = 0.241X There is a 2.16% of reference with a coverageData >= 1X There is a 0.15% 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 5782867 0.02320101340890942 0.4504655968500027 chr2 243199373 6186734 0.025438938940027613 0.26842187402022993 chr3 198022430 4919498 0.02484313519433127 0.16856428156777878 chr4 191154276 4764607 0.02492545340706896 0.186070359324321 chr5 180915260 4428194 0.0244766196063284 0.16733051014186198 chr6 171115067 4200405 0.024547253924752283 0.18589033120909113 chr7 159138663 4114156 0.025852649019679146 0.34652896607008377 chr8 146364022 3727323 0.025466114889901015 0.22262828248180494 chr9 141213431 3074019 0.021768602166461065 0.20437085771168387 chr10 135534747 3490586 0.02575417800425746 0.2276625083384673 chr11 135006516 3327134 0.024644247541355708 0.21596167119701856 chr12 133851895 3218800 0.024047474262504837 0.17071718378400336 chr13 115169878 2276813 0.01976917089379916 0.14998181955693085 chr14 107349540 2203795 0.020529151778386753 0.16023083050787287 chr15 102531392 2181025 0.021271777915587063 0.15629812593481418 chr16 90354753 2126208 0.02353177812350392 0.1732248258392222 chr17 81195210 1967130 0.024227168080481594 0.17792214817940302 chr18 78077248 2032887 0.026036868000265584 0.3544966153074194 chr19 59128983 1475389 0.024952044245374557 0.30205457092664406 chr20 63025520 1575811 0.02500274491983565 0.17171723707342196 chr21 48129895 998849 0.02075319299990162 0.16793744215410547 chr22 51304566 876972 0.017093449343280675 0.1402851304443092 chrMT 16571 10999 0.6637499245670146 0.9395699811157378 chrX 155270560 4042873 0.026037601719218376 0.1921343933727165 chrY 59373566 222031 0.003739559789957706 0.104616334547432