BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524450.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 = 5,419,907 number of mapped reads = 4,969,242 (91.69%) number of supplementary alignments = 10,126 (0.19%) number of secondary alignments = 0 number of mapped bases = 287,595,473 bp number of sequenced bases = 287,504,891 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 510,241 duplication rate = 7.54% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3632 >>>>>>> ACTG content number of A's = 75,576,066 bp (26.29%) number of C's = 50,345,874 bp (17.51%) number of T's = 90,322,066 bp (31.42%) number of G's = 71,254,717 bp (24.78%) number of N's = 6,168 bp (0%) GC percentage = 42.3% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 1,347,853 number of insertions = 20,241 mapped reads with insertion percentage = 0.41% number of deletions = 53,081 mapped reads with deletion percentage = 1.06% homopolymer indels = 43.71% >>>>>>> Coverage mean coverageData = 0.0929X std coverageData = 0.7227X There is a 6.75% of reference with a coverageData >= 1X There is a 1.6% of reference with a coverageData >= 2X There is a 0.47% of reference with a coverageData >= 3X There is a 0.16% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% 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 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% 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 28393371 0.11391494587289314 1.3904453093233482 chr2 243199373 22912969 0.09421475358820107 0.8758418158563462 chr3 198022430 15759077 0.0795822826737355 0.3761236860609678 chr4 191154276 16370517 0.08564033901077892 0.5122792899216627 chr5 180915260 15789774 0.08727718159319452 0.39499723883648324 chr6 171115067 12365726 0.07226555917486799 0.5307173943685748 chr7 159138663 14279005 0.08972681264765936 1.0514748037648838 chr8 146364022 26343644 0.17998715558663728 0.7179369812612749 chr9 141213431 11942449 0.08457020635664605 0.6015665629166607 chr10 135534747 15052691 0.11106149037928997 0.7424207527717263 chr11 135006516 9987057 0.07397462949121655 0.6933297050921179 chr12 133851895 13239615 0.09891242107554772 0.41925613964106406 chr13 115169878 6391633 0.05549743657799134 0.31942633800105236 chr14 107349540 6802121 0.06336423053140237 0.351071359609341 chr15 102531392 7631943 0.07443518371427163 0.402213756559767 chr16 90354753 8965996 0.09923103879217068 0.4726229779814903 chr17 81195210 9948435 0.1225249001757616 0.5106284229046318 chr18 78077248 6769940 0.086708230290084 1.1394258750176818 chr19 59128983 5801340 0.09811330595691119 0.9598591788093956 chr20 63025520 8281895 0.13140542116907564 0.5015610899658738 chr21 48129895 3858022 0.08015853764069089 0.4382234010827096 chr22 51304566 2325918 0.045335497039386316 0.2787359778353118 chrMT 16571 22843 1.3784925472210487 1.658614946417783 chrX 155270560 17413003 0.11214619822328199 0.5608227505090188 chrY 59373566 946489 0.015941252374836304 0.3860416625171307