BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717069.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 = 553,561 number of mapped reads = 505,327 (91.29%) number of supplementary alignments = 1,227 (0.22%) number of secondary alignments = 0 number of mapped bases = 29,045,978 bp number of sequenced bases = 29,036,855 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,089 duplication rate = 1.79% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2014 >>>>>>> ACTG content number of A's = 7,043,982 bp (24.26%) number of C's = 5,132,139 bp (17.67%) number of T's = 9,212,050 bp (31.73%) number of G's = 7,648,428 bp (26.34%) number of N's = 256 bp (0%) GC percentage = 44.01% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 141,696 number of insertions = 1,935 mapped reads with insertion percentage = 0.38% number of deletions = 5,737 mapped reads with deletion percentage = 1.13% homopolymer indels = 43.53% >>>>>>> Coverage mean coverageData = 0.0094X std coverageData = 0.1139X There is a 0.89% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% 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 2349446 0.00942603870182534 0.13311776181863094 chr2 243199373 2454363 0.01009197914338373 0.1387900930335789 chr3 198022430 1922754 0.00970977883667017 0.1027053642056561 chr4 191154276 1915895 0.010022768206346585 0.10770866942337518 chr5 180915260 1780034 0.009839048403103198 0.10317174779454036 chr6 171115067 1697559 0.009920569998666452 0.10979279780515969 chr7 159138663 1547987 0.00972728418611887 0.13841429133816602 chr8 146364022 1423197 0.00972368059139561 0.11289324455648977 chr9 141213431 1168648 0.008275756716087438 0.10113186483469924 chr10 135534747 1381962 0.010196366840157971 0.12715072890250476 chr11 135006516 1300086 0.009629801868229827 0.11021615899044628 chr12 133851895 1286077 0.009608209132937565 0.10228689972002875 chr13 115169878 938844 0.008151819002534673 0.09394520871984378 chr14 107349540 866898 0.008075470095167618 0.09490824716444539 chr15 102531392 845201 0.008243338781550922 0.09417023977809409 chr16 90354753 860349 0.009521900856726375 0.10678194768661825 chr17 81195210 832716 0.010255728139627942 0.10859215200682226 chr18 78077248 781137 0.010004668709634847 0.15217866479608172 chr19 59128983 616324 0.010423382387618606 0.12617579458429395 chr20 63025520 593737 0.009420580742530962 0.10210045836480036 chr21 48129895 388382 0.008069454545870087 0.09685640399728107 chr22 51304566 354871 0.006916947704030865 0.08666908332917746 chrMT 16571 4300 0.2594894695552471 0.5500805170853039 chrX 155270560 1648578 0.010617453817388177 0.11073475777192793 chrY 59373566 86633 0.001459117345250915 0.05044215325265053