BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524947.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 = 1,430,845 number of mapped reads = 1,334,221 (93.25%) number of supplementary alignments = 3,883 (0.27%) number of secondary alignments = 0 number of mapped bases = 79,134,550 bp number of sequenced bases = 79,107,570 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 34,964 duplication rate = 1.82% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.121 >>>>>>> ACTG content number of A's = 20,243,161 bp (25.59%) number of C's = 14,804,047 bp (18.71%) number of T's = 25,088,464 bp (31.71%) number of G's = 18,971,035 bp (23.98%) number of N's = 863 bp (0%) GC percentage = 42.7% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 379,229 number of insertions = 6,227 mapped reads with insertion percentage = 0.46% number of deletions = 15,751 mapped reads with deletion percentage = 1.17% homopolymer indels = 41.37% >>>>>>> Coverage mean coverageData = 0.0256X std coverageData = 0.2433X There is a 2.34% of reference with a coverageData >= 1X There is a 0.15% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 8407569 0.0337313863703473 0.4594723045592236 chr2 243199373 7635749 0.03139707518900552 0.2701455963281817 chr3 198022430 4435493 0.02239894238243617 0.1599346082851766 chr4 191154276 5229215 0.027355992810749366 0.18600568283917338 chr5 180915260 3476802 0.019217848179307814 0.15069450453812064 chr6 171115067 5361127 0.031330537362907966 0.2575020878649768 chr7 159138663 5027739 0.0315934475332371 0.3279636476484836 chr8 146364022 4935085 0.033717883210397155 0.2517158690984749 chr9 141213431 2183814 0.015464633813762375 0.18381020653769944 chr10 135534747 3983568 0.029391488811352562 0.23713090832831393 chr11 135006516 3357751 0.02487102918795416 0.21843041526058293 chr12 133851895 4360439 0.032576595198745596 0.19312971974982537 chr13 115169878 1543566 0.013402514848543991 0.12336323442060713 chr14 107349540 1809411 0.016855321410785738 0.14245420574764697 chr15 102531392 2135792 0.02083061546652951 0.16194508776716093 chr16 90354753 2462168 0.027250010854437286 0.18471633409740196 chr17 81195210 1980195 0.024388076587276514 0.2186121564415294 chr18 78077248 1583186 0.020277174728289604 0.2858890225447979 chr19 59128983 1819741 0.030775787231111348 0.29726188452588903 chr20 63025520 1879522 0.029821602423907013 0.18667755766593447 chr21 48129895 904311 0.01878896681573895 0.15496480704987828 chr22 51304566 1011329 0.019712261088028694 0.1480319231574535 chrMT 16571 48170 2.9068855229014545 2.369758072492645 chrX 155270560 3360580 0.021643381720269445 0.17875222369073296 chrY 59373566 202228 0.00340602752410054 0.09128223118520265