BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716440.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 = 1,222,694 number of mapped reads = 1,119,881 (91.59%) number of supplementary alignments = 3,468 (0.28%) number of secondary alignments = 0 number of mapped bases = 64,357,001 bp number of sequenced bases = 64,337,572 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 32,618 duplication rate = 1.99% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.761 >>>>>>> ACTG content number of A's = 15,573,783 bp (24.21%) number of C's = 11,755,996 bp (18.27%) number of T's = 21,035,928 bp (32.7%) number of G's = 15,970,633 bp (24.82%) number of N's = 1,232 bp (0%) GC percentage = 43.1% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 329,621 number of insertions = 4,384 mapped reads with insertion percentage = 0.39% number of deletions = 12,181 mapped reads with deletion percentage = 1.08% homopolymer indels = 43.56% >>>>>>> Coverage mean coverageData = 0.0208X std coverageData = 0.2121X There is a 1.92% of reference with a coverageData >= 1X There is a 0.11% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% 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 5398267 0.02165798816605556 0.3062729832182997 chr2 243199373 5031459 0.020688618304949332 0.3095025412147296 chr3 198022430 3763819 0.019007033698152275 0.1498829871452253 chr4 191154276 4005936 0.02095655971619489 0.1703391944118849 chr5 180915260 3663219 0.02024825877043208 0.15126481589965318 chr6 171115067 3450640 0.020165611716705226 0.17113708527777025 chr7 159138663 3690800 0.023192352696842753 0.2839718240684876 chr8 146364022 3426563 0.023411238316476436 0.25348195380790495 chr9 141213431 2132671 0.015102465713760612 0.15659317823942165 chr10 135534747 2832801 0.020900920706333703 0.22426275098734105 chr11 135006516 2326133 0.017229783190612816 0.17275528484711175 chr12 133851895 3208517 0.023970650546262344 0.1661593797056345 chr13 115169878 1977296 0.01716851692766402 0.14079319271388 chr14 107349540 2149177 0.02002036524795542 0.15352567252049343 chr15 102531392 2359886 0.023016229019888854 0.16279452667473518 chr16 90354753 2157339 0.023876320042621333 0.17458985483163464 chr17 81195210 2787995 0.0343369393342292 0.2026099069601959 chr18 78077248 1205616 0.015441322931873828 0.24622490989199736 chr19 59128983 1602997 0.02711017370280155 0.264883166175836 chr20 63025520 2044772 0.03244355619755299 0.1968065136098549 chr21 48129895 823559 0.017111173834889935 0.1594491234039456 chr22 51304566 581249 0.011329381482342136 0.11232507666549967 chrMT 16571 52968 3.1964274938144954 2.4181911029279384 chrX 155270560 3463600 0.022306868732875053 0.1718037515174391 chrY 59373566 219722 0.003700670429665619 0.15974980646259715