BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240185.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 = 1,415,650 number of mapped reads = 1,117,106 (78.91%) number of supplementary alignments = 10,432 (0.74%) number of secondary alignments = 0 number of mapped bases = 74,906,931 bp number of sequenced bases = 74,873,535 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 110,027 duplication rate = 7.8% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.1618 >>>>>>> ACTG content number of A's = 21,363,698 bp (28.53%) number of C's = 13,970,477 bp (18.66%) number of T's = 23,716,022 bp (31.67%) number of G's = 15,780,729 bp (21.08%) number of N's = 42,609 bp (0.06%) GC percentage = 39.74% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 671,455 number of insertions = 5,521 mapped reads with insertion percentage = 0.49% number of deletions = 19,247 mapped reads with deletion percentage = 1.71% homopolymer indels = 47.98% >>>>>>> Coverage mean coverageData = 0.0242X std coverageData = 0.3061X There is a 1.32% of reference with a coverageData >= 1X There is a 0.56% of reference with a coverageData >= 2X There is a 0.26% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.06% 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% 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 5924495 0.02376922864316555 0.445598056250865 chr2 243199373 7895948 0.032466975151288734 0.345972542151479 chr3 198022430 4745697 0.023965451792506535 0.25494447184043406 chr4 191154276 4939489 0.02584032700372342 0.2672889004644537 chr5 180915260 4097719 0.022649935666012918 0.2510011013276998 chr6 171115067 3953368 0.02310356457388992 0.2645625061815505 chr7 159138663 4308663 0.027074897569046436 0.3861956387829823 chr8 146364022 4275334 0.029210279559002555 0.39297922334555474 chr9 141213431 2860183 0.020254326941464937 0.2686033385466982 chr10 135534747 3596714 0.026537209679522257 0.30921952432533206 chr11 135006516 3259718 0.02414489386571534 0.2951033592516512 chr12 133851895 3685054 0.027530831745041787 0.2737656244748017 chr13 115169878 1997807 0.01734661036977047 0.21803752209203997 chr14 107349540 2457010 0.022887941578510724 0.2561700324988029 chr15 102531392 2144330 0.020913887524320357 0.24342999273847718 chr16 90354753 2207733 0.02443405495226134 0.26258654097914297 chr17 81195210 1709370 0.021052596575586172 0.2490596912607276 chr18 78077248 1845768 0.02364027994429312 0.39946024925608714 chr19 59128983 1245599 0.021065794417603968 0.3195018165296283 chr20 63025520 1476489 0.02342684360240106 0.25553364277337115 chr21 48129895 1243951 0.025845703590253 0.2714563889677028 chr22 51304566 640694 0.012488050283867522 0.17915106842013126 chrMT 16571 18218 1.0993905014784866 1.931056277516489 chrX 155270560 4162975 0.026811103147950262 0.2780851595406074 chrY 59373566 214605 0.0036144872955752735 0.09359766953839116