BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716903.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 = 3,903,679 number of mapped reads = 2,692,529 (68.97%) number of supplementary alignments = 19,098 (0.49%) number of secondary alignments = 0 number of mapped bases = 156,552,321 bp number of sequenced bases = 156,510,893 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 158,845 duplication rate = 4.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7463 >>>>>>> ACTG content number of A's = 41,735,800 bp (26.67%) number of C's = 29,564,478 bp (18.89%) number of T's = 47,475,523 bp (30.33%) number of G's = 37,733,107 bp (24.11%) number of N's = 1,985 bp (0%) GC percentage = 43% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 781,061 number of insertions = 10,702 mapped reads with insertion percentage = 0.4% number of deletions = 26,007 mapped reads with deletion percentage = 0.96% homopolymer indels = 40.05% >>>>>>> Coverage mean coverageData = 0.0506X std coverageData = 0.3902X There is a 4.16% of reference with a coverageData >= 1X There is a 0.64% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.03% 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 0.01% 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 12657070 0.050780495347291434 0.6729703666562573 chr2 243199373 12686914 0.05216672166338192 0.506608260368816 chr3 198022430 10382536 0.05243111096051089 0.2714707373993787 chr4 191154276 10023524 0.052436828564588325 0.316301718728274 chr5 180915260 9518084 0.05261073057076556 0.2718440568094424 chr6 171115067 8952947 0.05232120792729491 0.2969780213049451 chr7 159138663 8070377 0.05071286165072281 0.45917714037014656 chr8 146364022 8102016 0.0553552429708443 0.4158320211589293 chr9 141213431 6478651 0.04587843347563731 0.32293544832974463 chr10 135534747 7550532 0.05570919758311129 0.40708664392506977 chr11 135006516 7145640 0.05292811200312732 0.3517027702854465 chr12 133851895 7073172 0.05284327128876285 0.2773340840204605 chr13 115169878 4980491 0.0432447362668909 0.24871978560906643 chr14 107349540 4893351 0.04558334390627105 0.2629617966418827 chr15 102531392 4496692 0.04385673414050596 0.2593177788104744 chr16 90354753 4549189 0.05034808738838564 0.2825350711027375 chr17 81195210 4379968 0.05394367475618328 0.30784621607033447 chr18 78077248 4258903 0.05454729910562421 0.5962795583320578 chr19 59128983 3340136 0.0564889810467398 0.5244908583186224 chr20 63025520 3379346 0.053618692872347586 0.2827736469866692 chr21 48129895 2103117 0.043696687890135644 0.2858227993482902 chr22 51304566 1948356 0.037976269012781436 0.23015709346130914 chrMT 16571 31584 1.9059803270774245 1.8838635746440813 chrX 155270560 9069123 0.05840851607671151 0.3211356579700772 chrY 59373566 480602 0.00809454496972609 0.20282401994254626