BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231766.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 = 1,053,688 number of mapped reads = 707,136 (67.11%) number of supplementary alignments = 6,698 (0.64%) number of secondary alignments = 0 number of mapped bases = 45,915,358 bp number of sequenced bases = 45,879,228 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 57,282 duplication rate = 6.55% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1679 >>>>>>> ACTG content number of A's = 13,107,176 bp (28.57%) number of C's = 7,714,507 bp (16.81%) number of T's = 15,385,111 bp (33.53%) number of G's = 9,670,430 bp (21.08%) number of N's = 2,004 bp (0%) GC percentage = 37.89% >>>>>>> Mismatches and indels general error rate = 0.0099 number of mismatches = 446,965 number of insertions = 4,241 mapped reads with insertion percentage = 0.59% number of deletions = 20,358 mapped reads with deletion percentage = 2.82% homopolymer indels = 42.81% >>>>>>> Coverage mean coverageData = 0.0148X std coverageData = 0.3117X There is a 1.1% of reference with a coverageData >= 1X There is a 0.26% 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% 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 4477617 0.01796431632561509 0.2281002878885724 chr2 243199373 2493067 0.010251124290521916 0.19220705535310367 chr3 198022430 4792036 0.02419946063685816 0.2044183421061748 chr4 191154276 1848104 0.009668127957545663 0.13616486169593464 chr5 180915260 2788737 0.015414603500003262 0.16203927592873404 chr6 171115067 2928630 0.01711497445166532 0.1755523812339837 chr7 159138663 2522584 0.015851484186466994 0.19713887778277916 chr8 146364022 1902466 0.012998180659451951 1.1891147922644596 chr9 141213431 1786489 0.012650985018556769 0.1588942374652542 chr10 135534747 1868310 0.013784730789367245 0.16844831920698863 chr11 135006516 1769307 0.01310534522644818 0.15918680815161412 chr12 133851895 1840235 0.013748292469075616 0.15254101860786418 chr13 115169878 2734833 0.023746078814114918 0.20666655537541026 chr14 107349540 1768159 0.016471044030556627 0.16631259021343292 chr15 102531392 1325864 0.012931298153057358 0.14640110168359757 chr16 90354753 850844 0.009416704398494676 0.12841308387054545 chr17 81195210 1016088 0.012514137225582643 0.14596409094667542 chr18 78077248 1635396 0.02094587145284629 0.2666391407663514 chr19 59128983 527845 0.008927009618954549 0.15116712316553485 chr20 63025520 757896 0.01202522406796485 0.1462796773099724 chr21 48129895 708108 0.014712436002613344 0.16031556167957295 chr22 51304566 333888 0.0065079587653075555 0.10120101590724749 chrMT 16571 47302 2.8545048578842556 2.892704849944148 chrX 155270560 3057952 0.01969434514823673 0.1959717372835382 chrY 59373566 133601 0.0022501764505773497 0.07110136440506294