BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068121.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 = 1,446,339 number of mapped reads = 721,167 (49.86%) number of supplementary alignments = 6,637 (0.46%) number of secondary alignments = 0 number of mapped bases = 45,990,640 bp number of sequenced bases = 45,971,799 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 128,811 duplication rate = 12.11% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2471 >>>>>>> ACTG content number of A's = 12,246,460 bp (26.64%) number of C's = 8,227,529 bp (17.9%) number of T's = 14,796,328 bp (32.19%) number of G's = 10,655,404 bp (23.18%) number of N's = 46,078 bp (0.1%) GC percentage = 41.08% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 437,273 number of insertions = 3,447 mapped reads with insertion percentage = 0.47% number of deletions = 11,395 mapped reads with deletion percentage = 1.57% homopolymer indels = 47.18% >>>>>>> Coverage mean coverageData = 0.0149X std coverageData = 0.2756X There is a 0.72% of reference with a coverageData >= 1X There is a 0.3% of reference with a coverageData >= 2X There is a 0.17% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.02% 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% 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 3778470 0.015159320305163853 0.45890151372771404 chr2 243199373 3825367 0.015729345650903465 0.28053845083488654 chr3 198022430 3122230 0.015767052247566096 0.2457886303133302 chr4 191154276 3017726 0.015786861079686233 0.26196307171692146 chr5 180915260 2761587 0.015264533240590097 0.23991604565128638 chr6 171115067 2938255 0.017171223151261135 0.25739416475815025 chr7 159138663 2379083 0.014949748572413228 0.2616272795832004 chr8 146364022 2402459 0.01641427290102755 0.26540373959232566 chr9 141213431 1896386 0.013429218358131954 0.23110560213348688 chr10 135534747 2224474 0.016412573522566875 0.30332251025104473 chr11 135006516 2247954 0.016650707436965485 0.27117075666794754 chr12 133851895 2003458 0.01496772234715093 0.22669857224581252 chr13 115169878 1445221 0.012548602335065424 0.2197026980880641 chr14 107349540 1444220 0.013453434453468548 0.22250035906537244 chr15 102531392 1312476 0.012800723509147325 0.25198304014721934 chr16 90354753 1361979 0.015073684059542502 0.23394567066235586 chr17 81195210 1058955 0.013042087088634908 0.21418022273325746 chr18 78077248 1249547 0.016003983644505504 0.34165564970299017 chr19 59128983 855067 0.014461046962367 0.30544266871487386 chr20 63025520 884415 0.014032648996787333 0.2269669614441604 chr21 48129895 666633 0.013850705471100655 0.23554028579302053 chr22 51304566 477616 0.009309424818056154 0.17427007013842802 chrMT 16571 42472 2.5630318025466177 3.0920680020656683 chrX 155270560 2385318 0.015362332692044133 0.24648182752187248 chrY 59373566 209272 0.0035246661788850614 0.11824042293837406