BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716281.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 = 1,351,282 number of mapped reads = 1,224,984 (90.65%) number of supplementary alignments = 5,127 (0.38%) number of secondary alignments = 0 number of mapped bases = 69,894,661 bp number of sequenced bases = 69,877,600 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 30,507 duplication rate = 1.92% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.745 >>>>>>> ACTG content number of A's = 17,135,519 bp (24.52%) number of C's = 13,515,266 bp (19.34%) number of T's = 21,955,258 bp (31.42%) number of G's = 17,270,041 bp (24.71%) number of N's = 1,516 bp (0%) GC percentage = 44.06% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 339,293 number of insertions = 3,685 mapped reads with insertion percentage = 0.3% number of deletions = 10,056 mapped reads with deletion percentage = 0.82% homopolymer indels = 41.82% >>>>>>> Coverage mean coverageData = 0.0226X std coverageData = 0.199X There is a 2.07% of reference with a coverageData >= 1X There is a 0.14% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 5673086 0.022760569170256952 0.31137276405195463 chr2 243199373 5992386 0.024639808590295995 0.21907488495099178 chr3 198022430 4588311 0.023170663040545457 0.16277357748513793 chr4 191154276 4474059 0.02340548740850558 0.1747255480608129 chr5 180915260 4297672 0.02375516581630538 0.16636815239395303 chr6 171115067 3925656 0.022941615071219883 0.1681342749161999 chr7 159138663 3835779 0.02410337580880644 0.2180483965929954 chr8 146364022 3460709 0.02364453335396864 0.19001035122396173 chr9 141213431 2983683 0.021128889645064992 0.19677744500021863 chr10 135534747 3365553 0.02483166180256344 0.19406425722025478 chr11 135006516 3074213 0.02277084907516612 0.19362912346196484 chr12 133851895 3157489 0.023589423220343648 0.16553894783756382 chr13 115169878 2146901 0.018641167615025173 0.14573911028897585 chr14 107349540 2124639 0.01979178485534265 0.15580239364066528 chr15 102531392 2077597 0.02026303319865198 0.1539313586940467 chr16 90354753 2105978 0.023307882873632557 0.17179261904194298 chr17 81195210 1942452 0.023923233895201453 0.1699587887073682 chr18 78077248 1850500 0.023700886588625663 0.32379095695393073 chr19 59128983 1389676 0.02350245056641681 0.23189530038063658 chr20 63025520 1563344 0.024804936159193925 0.17102143280922305 chr21 48129895 912917 0.018967774602458617 0.15755257265035463 chr22 51304566 816304 0.01591094250753432 0.1346487585662114 chrMT 16571 11428 0.6896385251342707 0.9409841367749158 chrX 155270560 3926137 0.02528577857901717 0.18693553157458137 chrY 59373566 198192 0.003338051145521561 0.08239221703484116