BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525095.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 = 2,155,945 number of mapped reads = 1,876,340 (87.03%) number of supplementary alignments = 51,671 (2.4%) number of secondary alignments = 0 number of mapped bases = 144,439,798 bp number of sequenced bases = 144,382,155 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 65,612 duplication rate = 2.03% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2602 >>>>>>> ACTG content number of A's = 38,846,226 bp (26.91%) number of C's = 25,917,468 bp (17.95%) number of T's = 45,358,441 bp (31.42%) number of G's = 34,255,002 bp (23.73%) number of N's = 5,018 bp (0%) GC percentage = 41.68% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 1,074,840 number of insertions = 12,899 mapped reads with insertion percentage = 0.68% number of deletions = 33,575 mapped reads with deletion percentage = 1.76% homopolymer indels = 43.2% >>>>>>> Coverage mean coverageData = 0.0467X std coverageData = 0.493X There is a 4.05% of reference with a coverageData >= 1X There is a 0.41% of reference with a coverageData >= 2X There is a 0.06% 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% 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 13896247 0.05575210582925689 0.8951525994918571 chr2 243199373 12163581 0.050014853451123 0.6820847551519881 chr3 198022430 9447209 0.047707772296299966 0.2434480419408836 chr4 191154276 9311602 0.048712496496808685 0.2605737171590583 chr5 180915260 8492608 0.046942463560011465 0.2497746075384987 chr6 171115067 8058694 0.04709517485096739 0.29005079634467407 chr7 159138663 7764691 0.048791983378671466 0.6982692384159428 chr8 146364022 7291805 0.0498196544503266 0.6373169405395248 chr9 141213431 5852270 0.04144272933925102 0.44257370889042513 chr10 135534747 6575255 0.04851342659753517 0.4721768474410793 chr11 135006516 7915895 0.05863342921907562 0.5717490656738695 chr12 133851895 6295607 0.04703412678617662 0.2437362210624416 chr13 115169878 5347684 0.04643300915887052 0.23911778945809342 chr14 107349540 4188630 0.03901861153759951 0.2791623633555308 chr15 102531392 3930712 0.03833666863705508 0.21537250949101047 chr16 90354753 3023819 0.03346607565846591 0.23970038431942203 chr17 81195210 4089691 0.05036862396193076 0.31531513637569036 chr18 78077248 3842196 0.049210187326274614 0.833405038279599 chr19 59128983 2516565 0.042560600103675045 0.6400876224879869 chr20 63025520 2721743 0.043184776579391966 0.2420981238920883 chr21 48129895 1902035 0.03951878556975867 0.2454865079767739 chr22 51304566 1402689 0.02734043203873901 0.1826523926128413 chrMT 16571 15735 0.9495504194073985 1.1079046211648693 chrX 155270560 8065557 0.05194517878984915 0.36938272485517415 chrY 59373566 327278 0.005512183654254488 0.1260908639387303