BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004063.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 = 2,139,374 number of mapped reads = 1,455,972 (68.06%) number of supplementary alignments = 17,270 (0.81%) number of secondary alignments = 0 number of mapped bases = 93,386,572 bp number of sequenced bases = 93,340,446 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 250,004 duplication rate = 11.9% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.363 >>>>>>> ACTG content number of A's = 25,814,203 bp (27.66%) number of C's = 17,032,000 bp (18.25%) number of T's = 29,833,854 bp (31.96%) number of G's = 20,597,613 bp (22.07%) number of N's = 62,776 bp (0.07%) GC percentage = 40.31% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 879,682 number of insertions = 8,210 mapped reads with insertion percentage = 0.56% number of deletions = 26,700 mapped reads with deletion percentage = 1.81% homopolymer indels = 44.79% >>>>>>> Coverage mean coverageData = 0.0302X std coverageData = 0.4369X There is a 1.37% of reference with a coverageData >= 1X There is a 0.67% of reference with a coverageData >= 2X There is a 0.37% of reference with a coverageData >= 3X There is a 0.21% of reference with a coverageData >= 4X There is a 0.12% of reference with a coverageData >= 5X There is a 0.07% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% 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 4890852 0.01962222593619937 0.319793516296444 chr2 243199373 3798307 0.015618078916675496 0.4072964261942821 chr3 198022430 4103903 0.020724435105659494 0.2776305392004395 chr4 191154276 10172592 0.05321665940656227 0.5327342845407571 chr5 180915260 6396609 0.03535693451177087 0.36544233416096367 chr6 171115067 2325147 0.013588207285101317 0.23568750673879021 chr7 159138663 3714310 0.023340085495125718 0.35545267061869157 chr8 146364022 3904818 0.026678810452475814 0.40205409871385506 chr9 141213431 5675255 0.040189201266556576 0.5939652811639653 chr10 135534747 7686997 0.05671606115884069 0.6255840574166416 chr11 135006516 3680559 0.02726208415007169 0.3781377050980876 chr12 133851895 2294635 0.017143089382485023 0.2708388084253016 chr13 115169878 1116270 0.009692378071287007 0.18109915959675793 chr14 107349540 1828012 0.01702859648956111 0.35028104682698424 chr15 102531392 11186772 0.10910582390220548 0.7362295179920183 chr16 90354753 2675168 0.029607385457630548 0.4468713022232758 chr17 81195210 1490960 0.01836265957068157 0.2586875553851646 chr18 78077248 2151542 0.027556580887687025 1.0264844344647994 chr19 59128983 1172768 0.01983406344059731 0.34308016049595114 chr20 63025520 1123861 0.017831840181564546 0.28139923215312856 chr21 48129895 3084477 0.06408651005783411 0.5366643520117675 chr22 51304566 1133489 0.02209333570817069 0.27390599222725037 chrMT 16571 42078 2.5392553255687647 3.19427436855109 chrX 155270560 7360751 0.0474059667202849 0.4582426411984125 chrY 59373566 376440 0.006340195230988821 0.2628049131004372