BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238316.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 = 1,466,559 number of mapped reads = 1,227,162 (83.68%) number of supplementary alignments = 14,146 (0.96%) number of secondary alignments = 0 number of mapped bases = 80,359,707 bp number of sequenced bases = 80,330,722 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 98,339 duplication rate = 6.5% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.8114 >>>>>>> ACTG content number of A's = 22,178,891 bp (27.61%) number of C's = 15,843,090 bp (19.72%) number of T's = 24,249,929 bp (30.19%) number of G's = 18,042,629 bp (22.46%) number of N's = 16,183 bp (0.02%) GC percentage = 42.18% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 616,925 number of insertions = 5,537 mapped reads with insertion percentage = 0.45% number of deletions = 17,854 mapped reads with deletion percentage = 1.44% homopolymer indels = 47.36% >>>>>>> Coverage mean coverageData = 0.026X std coverageData = 0.2647X There is a 1.71% of reference with a coverageData >= 1X There is a 0.53% of reference with a coverageData >= 2X There is a 0.19% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% 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 7936924 0.03184314634064643 0.2900808359700451 chr2 243199373 13048083 0.05365179539340342 0.40783261896630374 chr3 198022430 10712929 0.05409957346751072 0.3427223063104789 chr4 191154276 1720585 0.009001028049197288 0.15197025782835444 chr5 180915260 3328334 0.01839719877693015 0.20510130041336563 chr6 171115067 5140128 0.03003901462400152 0.27125199218814644 chr7 159138663 5083375 0.031943054592585084 0.33361725671193915 chr8 146364022 1642568 0.011222484716906728 0.18258700817536053 chr9 141213431 6897173 0.04884218838928997 0.3290388568140923 chr10 135534747 659065 0.004862701370593919 0.1421295861046084 chr11 135006516 3346785 0.024789803478818755 0.23560850738184577 chr12 133851895 4804752 0.03589603270091918 0.2822364312342842 chr13 115169878 442509 0.003842228607726753 0.11566140273550723 chr14 107349540 3944893 0.03674811275390654 0.35625687997528127 chr15 102531392 3628984 0.035393882100030395 0.36998142685475016 chr16 90354753 1155510 0.012788591210027435 0.16232641488486468 chr17 81195210 1422227 0.0175161441173685 0.2137886190632607 chr18 78077248 1843803 0.023615112561344374 0.2239960371588597 chr19 59128983 449937 0.0076094155044066965 0.13075363256137523 chr20 63025520 1082911 0.017182103376536997 0.1926995157741164 chr21 48129895 565851 0.011756747028016578 0.15241777935720596 chr22 51304566 318270 0.0062035414157874365 0.11278108458862499 chrMT 16571 2893 0.17458210126123952 0.6460275824304655 chrX 155270560 1073728 0.006915206591642357 0.14686333375015134 chrY 59373566 107490 0.0018104016187944648 0.06223217969626711