BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240217.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 = 2,742,302 number of mapped reads = 1,959,136 (71.44%) number of supplementary alignments = 17,710 (0.65%) number of secondary alignments = 0 number of mapped bases = 122,586,177 bp number of sequenced bases = 122,529,671 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 251,221 duplication rate = 10.21% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9852 >>>>>>> ACTG content number of A's = 32,827,286 bp (26.79%) number of C's = 22,784,068 bp (18.59%) number of T's = 38,586,126 bp (31.49%) number of G's = 28,321,805 bp (23.11%) number of N's = 10,386 bp (0.01%) GC percentage = 41.71% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 1,066,603 number of insertions = 8,462 mapped reads with insertion percentage = 0.43% number of deletions = 32,434 mapped reads with deletion percentage = 1.64% homopolymer indels = 46.22% >>>>>>> Coverage mean coverageData = 0.0396X std coverageData = 0.4138X There is a 2.38% of reference with a coverageData >= 1X There is a 0.88% of reference with a coverageData >= 2X There is a 0.36% of reference with a coverageData >= 3X There is a 0.15% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 10348570 0.04151873306666706 0.765036854879187 chr2 243199373 10265597 0.042210622804525075 0.4741005285950319 chr3 198022430 7406101 0.03740031369173684 0.2968682507519076 chr4 191154276 7119549 0.03724504180068669 0.340398617479465 chr5 180915260 7280966 0.040245173348008347 0.30926376755494805 chr6 171115067 6969389 0.04072925384180225 0.34336409943666163 chr7 159138663 7111185 0.04468546402202713 0.433163175996252 chr8 146364022 5545979 0.037891682151232495 0.408961499603363 chr9 141213431 5610456 0.03973032848412273 0.35938488320534107 chr10 135534747 5898942 0.04352346634771082 0.40302444660811215 chr11 135006516 6594182 0.0488434350827926 0.38546821742793347 chr12 133851895 4841025 0.03616702624942292 0.2944418503919147 chr13 115169878 3256791 0.028278149257047924 0.2554744923002759 chr14 107349540 4027197 0.0375148044416399 0.3128813252070355 chr15 102531392 3437849 0.03352972131696018 0.32034669268846716 chr16 90354753 4773646 0.05283226218326334 0.36870471583574294 chr17 81195210 2857786 0.03519648511285333 0.306045127236792 chr18 78077248 3580061 0.04585280720959837 0.554101680424986 chr19 59128983 2436981 0.04121466117555243 0.5567982872901834 chr20 63025520 2668795 0.04234467244379737 0.3197857383358128 chr21 48129895 1604461 0.033336058597260604 0.29113424293527745 chr22 51304566 1379105 0.02688074585798075 0.24725910619324792 chrMT 16571 100177 6.045320137589766 5.9638121975899745 chrX 155270560 7107326 0.04577381571883298 0.3520863012033542 chrY 59373566 364061 0.0061317017744900145 0.14617990882810125