BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008821.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 = 986,780 number of mapped reads = 712,642 (72.22%) number of supplementary alignments = 3,377 (0.34%) number of secondary alignments = 0 number of mapped bases = 43,613,250 bp number of sequenced bases = 43,589,646 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 26,859 duplication rate = 3.27% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9183 >>>>>>> ACTG content number of A's = 12,428,009 bp (28.51%) number of C's = 8,092,554 bp (18.57%) number of T's = 13,082,153 bp (30.01%) number of G's = 9,971,919 bp (22.88%) number of N's = 15,011 bp (0.03%) GC percentage = 41.44% >>>>>>> Mismatches and indels general error rate = 0.0109 number of mismatches = 469,701 number of insertions = 3,447 mapped reads with insertion percentage = 0.48% number of deletions = 14,875 mapped reads with deletion percentage = 2.06% homopolymer indels = 47.88% >>>>>>> Coverage mean coverageData = 0.0141X std coverageData = 0.1662X There is a 1.1% of reference with a coverageData >= 1X There is a 0.22% of reference with a coverageData >= 2X There is a 0.05% 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 3722177 0.014933471319214887 0.21923302134124997 chr2 243199373 3726600 0.015323230294676788 0.17968876282659635 chr3 198022430 3007274 0.015186532151938546 0.15399502920088087 chr4 191154276 2547367 0.013326236029373467 0.14672847548146986 chr5 180915260 2284277 0.012626226223260548 0.14018576745123015 chr6 171115067 2647008 0.01546916964360596 0.16383129313978775 chr7 159138663 2437941 0.015319602125851718 0.1859466967103126 chr8 146364022 3002359 0.020512957754057894 0.204869869430038 chr9 141213431 1489223 0.01054590196877236 0.1459188991471691 chr10 135534747 2114262 0.015599409352938845 0.18037831188799233 chr11 135006516 1874801 0.013886744547944634 0.16013738224591123 chr12 133851895 2338033 0.017467313406358573 0.17085656909389058 chr13 115169878 1214012 0.010541054840745773 0.12871770398122293 chr14 107349540 1488429 0.013865257363934675 0.1489807987928225 chr15 102531392 1225830 0.011955655493295166 0.1361842709825334 chr16 90354753 1068851 0.011829493906092578 0.13775322541342946 chr17 81195210 1156418 0.014242441148929844 0.15329903706759185 chr18 78077248 1079715 0.013828804519339617 0.21863885218431114 chr19 59128983 762713 0.012899139496446268 0.16214212586513793 chr20 63025520 986397 0.015650755440018583 0.15746843145991218 chr21 48129895 509257 0.01058088740895861 0.13241226003816076 chr22 51304566 460024 0.008966531360970873 0.1156676167562977 chrMT 16571 19212 1.1593748114175366 1.3209745423190637 chrX 155270560 2319700 0.014939728432743464 0.15569581299357646 chrY 59373566 131370 0.002212600806224103 0.07076684901467609