BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524335.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 = 3,021,312 number of mapped reads = 2,758,486 (91.3%) number of supplementary alignments = 12,779 (0.42%) number of secondary alignments = 0 number of mapped bases = 160,943,120 bp number of sequenced bases = 160,901,343 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 122,050 duplication rate = 3.14% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1079 >>>>>>> ACTG content number of A's = 37,863,091 bp (23.53%) number of C's = 30,849,761 bp (19.17%) number of T's = 51,045,595 bp (31.72%) number of G's = 41,121,346 bp (25.56%) number of N's = 21,550 bp (0.01%) GC percentage = 44.73% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 810,816 number of insertions = 8,932 mapped reads with insertion percentage = 0.32% number of deletions = 25,620 mapped reads with deletion percentage = 0.92% homopolymer indels = 42% >>>>>>> Coverage mean coverageData = 0.052X std coverageData = 0.4384X There is a 4.47% of reference with a coverageData >= 1X There is a 0.51% of reference with a coverageData >= 2X There is a 0.09% 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 0.01% 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 13702435 0.054974527024347915 0.8664244146862875 chr2 243199373 10276631 0.04225599298728455 0.5735030444075863 chr3 198022430 11122217 0.05616645043695303 0.2719452365055175 chr4 191154276 8482632 0.0443758422647056 0.2875587300700676 chr5 180915260 9484220 0.05242354901405222 0.2601906045477447 chr6 171115067 10140977 0.05926407988374279 0.3138978956973951 chr7 159138663 7502056 0.04714163018951592 0.5578766054155434 chr8 146364022 15758529 0.10766668464467313 0.5206640082889924 chr9 141213431 6710207 0.04751819251527144 0.32295734056082903 chr10 135534747 8313519 0.06133865435997752 0.4424585505654103 chr11 135006516 7814743 0.05788419130821804 0.3579060008281885 chr12 133851895 6441761 0.04812603512262564 0.25397458719800664 chr13 115169878 4118373 0.03575911576462727 0.21529432437636928 chr14 107349540 3395381 0.031629208657997045 0.2186697916918169 chr15 102531392 4965452 0.04842860223725432 0.25039343827007865 chr16 90354753 5667904 0.06272945043632625 0.31001138133265205 chr17 81195210 4786794 0.0589541427382231 0.3168727592638388 chr18 78077248 3683570 0.047178532726973164 0.6160344111905058 chr19 59128983 2990031 0.050567942289824266 0.583836586867793 chr20 63025520 3768866 0.05979904648148877 0.2852740195679263 chr21 48129895 2354270 0.04891492075767047 0.28784938525134823 chr22 51304566 1238975 0.024149410015475038 0.17563880136844695 chrMT 16571 31403 1.8950576308007965 1.8355816701113692 chrX 155270560 7719564 0.049716855532690805 0.2958818845232702 chrY 59373566 472610 0.007959939613531045 0.23333730944097886