BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237576.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 = 2,404,437 number of mapped reads = 1,948,419 (81.03%) number of supplementary alignments = 11,868 (0.49%) number of secondary alignments = 0 number of mapped bases = 123,180,592 bp number of sequenced bases = 123,109,848 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 115,512 duplication rate = 3.96% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.0607 >>>>>>> ACTG content number of A's = 31,764,392 bp (25.8%) number of C's = 23,602,269 bp (19.17%) number of T's = 37,122,540 bp (30.15%) number of G's = 30,599,909 bp (24.86%) number of N's = 20,738 bp (0.02%) GC percentage = 44.03% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 1,140,106 number of insertions = 11,681 mapped reads with insertion percentage = 0.59% number of deletions = 43,186 mapped reads with deletion percentage = 2.19% homopolymer indels = 46.6% >>>>>>> Coverage mean coverageData = 0.0398X std coverageData = 0.3608X There is a 3.1% of reference with a coverageData >= 1X There is a 0.47% of reference with a coverageData >= 2X There is a 0.16% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.04% 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 0.01% 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 10526346 0.04223197502083656 0.4491585223861654 chr2 243199373 10587099 0.04353259167325238 0.502111561864633 chr3 198022430 8448215 0.042662919549063205 0.28601456482714216 chr4 191154276 7748378 0.04053468309544904 0.29555548538087234 chr5 180915260 6879252 0.03802471941836195 0.25731454604064163 chr6 171115067 6543423 0.038239899704448584 0.29230713068749564 chr7 159138663 7221605 0.04537932431919451 0.5159533910260531 chr8 146364022 6506608 0.04445496858510762 0.3521857518578785 chr9 141213431 5077881 0.03595890960258589 0.3959287402998904 chr10 135534747 5425412 0.040029675932475084 0.3546144181977439 chr11 135006516 5176316 0.0383412308780711 0.373876252144765 chr12 133851895 7070800 0.05282555020980465 0.33087968627090125 chr13 115169878 4053819 0.03519860462125349 0.2610772635381655 chr14 107349540 3488076 0.03249269628915038 0.27951068298971926 chr15 102531392 3823988 0.03729577766778003 0.2728885916926823 chr16 90354753 3412424 0.037766956210925615 0.2981147735751706 chr17 81195210 3167089 0.039005860074750716 0.29190265364151335 chr18 78077248 3174112 0.04065348204895746 0.5367216206937473 chr19 59128983 2518288 0.04258973978970685 0.3930355791992434 chr20 63025520 2526777 0.04009133125756043 0.2844601325430114 chr21 48129895 1502920 0.03122633032962154 0.2741301447244387 chr22 51304566 1411205 0.027506421163371698 0.226781852723842 chrMT 16571 124437 7.509323516987508 5.695384652798458 chrX 155270560 6325397 0.040737902922485754 0.29626908594452667 chrY 59373566 440725 0.0074229161172498885 0.1676730639862181