BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231740.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 = 1,908,691 number of mapped reads = 1,481,996 (77.64%) number of supplementary alignments = 10,635 (0.56%) number of secondary alignments = 0 number of mapped bases = 99,290,980 bp number of sequenced bases = 99,240,962 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 189,300 duplication rate = 9.4% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.0323 >>>>>>> ACTG content number of A's = 28,541,896 bp (28.76%) number of C's = 17,141,046 bp (17.27%) number of T's = 32,985,115 bp (33.24%) number of G's = 20,542,668 bp (20.7%) number of N's = 30,237 bp (0.03%) GC percentage = 37.97% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 837,171 number of insertions = 8,515 mapped reads with insertion percentage = 0.57% number of deletions = 28,484 mapped reads with deletion percentage = 1.9% homopolymer indels = 45.27% >>>>>>> Coverage mean coverageData = 0.0321X std coverageData = 0.6359X There is a 1.77% of reference with a coverageData >= 1X There is a 0.73% of reference with a coverageData >= 2X There is a 0.34% of reference with a coverageData >= 3X There is a 0.16% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.04% 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 5807483 0.02329977344369385 0.5249202286948247 chr2 243199373 4370489 0.017970807021776326 0.3197278776660538 chr3 198022430 12079228 0.06099929184789824 0.40938506127694374 chr4 191154276 5320707 0.02783462191554637 0.28623736329573607 chr5 180915260 4214159 0.023293551909330367 0.2506000755197086 chr6 171115067 6528327 0.038151678367399404 0.3391496215431444 chr7 159138663 7181372 0.04512650706384281 0.5759951240384602 chr8 146364022 7051747 0.048179510945661225 2.400544154835768 chr9 141213431 2949730 0.0208884521756291 0.2934144408287305 chr10 135534747 3486109 0.025721145884457217 0.3150295969837308 chr11 135006516 5501702 0.04075138121481485 0.4364555011005148 chr12 133851895 3789388 0.028310305207109695 0.27563809490328206 chr13 115169878 5492325 0.047688901780376984 0.36665425591121 chr14 107349540 4396764 0.040957455430176974 0.34326280059759656 chr15 102531392 2548332 0.024854163688716915 0.2532610829537781 chr16 90354753 2154483 0.023844711301463022 0.2694680922515005 chr17 81195210 1099142 0.013537030078498474 0.21387571186016613 chr18 78077248 3144213 0.04027054078545391 0.6508092997145674 chr19 59128983 2037556 0.034459513704133894 0.38312165685880417 chr20 63025520 1542723 0.02447775123473793 0.27172745290144895 chr21 48129895 2503926 0.052024339550294056 0.38323774346625644 chr22 51304566 297629 0.005801218550411283 0.11180184368537881 chrMT 16571 187103 11.290990284231489 9.354446227676844 chrX 155270560 5335933 0.03436538774639571 0.3278792855233997 chrY 59373566 270410 0.004554383679767525 0.11869569528920687