BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080774.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 3,222,195 number of mapped reads = 2,878,697 (89.34%) number of supplementary alignments = 36,036 (1.12%) number of secondary alignments = 0 number of mapped bases = 192,112,168 bp number of sequenced bases = 192,045,584 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 144,179 duplication rate = 4.14% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4218 >>>>>>> ACTG content number of A's = 55,298,567 bp (28.79%) number of C's = 36,757,652 bp (19.14%) number of T's = 58,756,523 bp (30.6%) number of G's = 41,228,922 bp (21.47%) number of N's = 3,920 bp (0%) GC percentage = 40.61% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 1,431,910 number of insertions = 14,576 mapped reads with insertion percentage = 0.5% number of deletions = 42,217 mapped reads with deletion percentage = 1.45% homopolymer indels = 47.41% >>>>>>> Coverage mean coverageData = 0.0621X std coverageData = 0.4209X There is a 4.76% of reference with a coverageData >= 1X There is a 1.03% of reference with a coverageData >= 2X There is a 0.25% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.02% 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 24861868 0.0997464636206463 0.7051062556069904 chr2 243199373 15288745 0.06286506750163373 0.4683158055958485 chr3 198022430 10607816 0.05356875986220349 0.28727083326624636 chr4 191154276 11654007 0.060966499122415654 0.3133577316562689 chr5 180915260 14536014 0.08034708625463656 0.35356747122334187 chr6 171115067 13560824 0.07924973666988659 0.4039904259857355 chr7 159138663 14160348 0.08898119245855421 0.5372241590750008 chr8 146364022 8652125 0.059113741763669216 0.6172311111924471 chr9 141213431 6634170 0.04697973806754968 0.3311054495460031 chr10 135534747 7428316 0.0548074657194734 0.3862489911368696 chr11 135006516 7929730 0.05873590575435633 0.4283580674911724 chr12 133851895 8000107 0.05976835068341767 0.3051351080567589 chr13 115169878 7806128 0.06777925040434618 0.3268741522737433 chr14 107349540 5324087 0.04959580637234216 0.28472920027101356 chr15 102531392 4358756 0.04251142908505524 0.26017029020506544 chr16 90354753 4271583 0.047275686758836026 0.2858009499868492 chr17 81195210 4509218 0.055535517427690625 0.31526132344372765 chr18 78077248 2561157 0.03280285954750864 0.5312124866898656 chr19 59128983 2761128 0.046696693565657976 0.4662461467493271 chr20 63025520 2955486 0.04689348060912468 0.27693311507891877 chr21 48129895 2864582 0.05951772801498944 0.31462716493858367 chr22 51304566 1672024 0.032590159714049625 0.22005201969642807 chrMT 16571 186800 11.272705328586085 6.854044397446244 chrX 155270560 9102027 0.05862043004159964 0.31626876649671076 chrY 59373566 425122 0.007160122401945674 0.136498502816012