BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716629.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 = 896,909 number of mapped reads = 807,905 (90.08%) number of supplementary alignments = 3,212 (0.36%) number of secondary alignments = 0 number of mapped bases = 46,558,841 bp number of sequenced bases = 46,544,508 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 23,494 duplication rate = 2.24% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1612 >>>>>>> ACTG content number of A's = 11,145,289 bp (23.95%) number of C's = 9,066,879 bp (19.48%) number of T's = 15,355,878 bp (32.99%) number of G's = 10,975,237 bp (23.58%) number of N's = 1,225 bp (0%) GC percentage = 43.06% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 239,736 number of insertions = 3,755 mapped reads with insertion percentage = 0.46% number of deletions = 9,007 mapped reads with deletion percentage = 1.1% homopolymer indels = 40.31% >>>>>>> Coverage mean coverageData = 0.015X std coverageData = 0.1672X There is a 1.4% of reference with a coverageData >= 1X There is a 0.08% of reference with a coverageData >= 2X There is a 0.01% 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 3773211 0.015138221059838402 0.2797100685286399 chr2 243199373 3908618 0.01607166150054178 0.20798877886046996 chr3 198022430 3062111 0.015463455326752631 0.13157649603973043 chr4 191154276 3005572 0.01572327892890034 0.13971037359123306 chr5 180915260 2810060 0.015532465310002042 0.1319186677735227 chr6 171115067 2696378 0.01575768894740286 0.14696007270050687 chr7 159138663 2580529 0.016215600604863697 0.19174459890663054 chr8 146364022 2307766 0.015767303798197074 0.16321574959702453 chr9 141213431 1943420 0.013762288659355639 0.14579000002214185 chr10 135534747 2234624 0.016487462067568546 0.16707541972274442 chr11 135006516 2128802 0.015768142628019524 0.1505417976816378 chr12 133851895 2104423 0.015722026199180818 0.13338044265048937 chr13 115169878 1443840 0.012536611352492706 0.11918830486269034 chr14 107349540 1390593 0.01295387944838888 0.12204229763262951 chr15 102531392 1355099 0.013216430339695379 0.12229719210015011 chr16 90354753 1347484 0.01491326084417496 0.1335587687006766 chr17 81195210 1257401 0.015486147520278598 0.13571982642897376 chr18 78077248 1222096 0.01565239594510298 0.21763759294779766 chr19 59128983 984059 0.01664258287682709 0.21170352597050657 chr20 63025520 1012734 0.01606863378517147 0.1362365270879162 chr21 48129895 620800 0.012898428305318347 0.1265960078778615 chr22 51304566 571961 0.011148344964072009 0.11176381833021187 chrMT 16571 17187 1.037173375173496 1.2172243500844226 chrX 155270560 2629954 0.016937879273443722 0.1453840569396538 chrY 59373566 150119 0.002528381064394886 0.07941829095692478