BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9867845.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 = 2,616,665 number of mapped reads = 2,409,374 (92.08%) number of supplementary alignments = 10,040 (0.38%) number of secondary alignments = 0 number of mapped bases = 142,119,846 bp number of sequenced bases = 142,077,784 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 134,284 duplication rate = 4.15% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8356 >>>>>>> ACTG content number of A's = 34,339,859 bp (24.17%) number of C's = 26,715,897 bp (18.8%) number of T's = 45,440,747 bp (31.98%) number of G's = 35,562,744 bp (25.03%) number of N's = 18,537 bp (0.01%) GC percentage = 43.83% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 716,422 number of insertions = 9,661 mapped reads with insertion percentage = 0.4% number of deletions = 26,331 mapped reads with deletion percentage = 1.08% homopolymer indels = 44.61% >>>>>>> Coverage mean coverageData = 0.0459X std coverageData = 0.4094X There is a 3.96% of reference with a coverageData >= 1X There is a 0.45% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 11563610 0.04639350527435596 0.7579911632754417 chr2 243199373 11993168 0.04931414029591269 0.5619345691148873 chr3 198022430 9341524 0.047174070129328276 0.2453486658014313 chr4 191154276 9047257 0.04732960825841008 0.2936998305130782 chr5 180915260 8474189 0.04684065346394771 0.246954426284223 chr6 171115067 8073819 0.04718356566461795 0.2935155024410209 chr7 159138663 7972589 0.05009837866992762 0.5187707007797103 chr8 146364022 7167432 0.04896990327308715 0.41596413558287804 chr9 141213431 5943665 0.042089941147311974 0.3382728225062285 chr10 135534747 6919987 0.05105692195669941 0.41728789761104396 chr11 135006516 6512579 0.0482389975903089 0.34798524206533155 chr12 133851895 6149483 0.04594244257804494 0.24534675447739412 chr13 115169878 4416676 0.038349228780115575 0.2223023289899287 chr14 107349540 4235189 0.03945232555258271 0.2327465862378855 chr15 102531392 4120038 0.040183186043158375 0.22810895305198148 chr16 90354753 4225342 0.04676391512021509 0.27083899904315845 chr17 81195210 3945780 0.04859621645168477 0.2715859288322598 chr18 78077248 3844486 0.049239517253476965 0.6767223168130786 chr19 59128983 3021654 0.051102756155978535 0.5737129556197379 chr20 63025520 3052877 0.04843874354388508 0.25822931771840674 chr21 48129895 1890365 0.03927631672581043 0.27405388170127826 chr22 51304566 1778931 0.03467393136119697 0.21165254789957297 chrMT 16571 24573 1.4828917989258343 1.519328076599744 chrX 155270560 7942857 0.05115494527745633 0.28913744276800063 chrY 59373566 461776 0.007777467838128503 0.2731824742919318