BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514763.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP106579/SRP106579.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 = 18,826,883 number of mapped reads = 15,725,907 (83.53%) number of supplementary alignments = 2,539,897 (13.49%) number of secondary alignments = 0 number of mapped bases = 1,484,318,127 bp number of sequenced bases = 1,483,028,137 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,161,943 duplication rate = 35.34% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2564 >>>>>>> ACTG content number of A's = 463,229,854 bp (31.24%) number of C's = 274,972,590 bp (18.54%) number of T's = 458,508,304 bp (30.92%) number of G's = 286,220,270 bp (19.3%) number of N's = 97,119 bp (0.01%) GC percentage = 37.84% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 8,426,015 number of insertions = 881,248 mapped reads with insertion percentage = 5.35% number of deletions = 423,454 mapped reads with deletion percentage = 2.49% homopolymer indels = 46.95% >>>>>>> Coverage mean coverageData = 0.4795X std coverageData = 23.5729X There is a 2.89% of reference with a coverageData >= 1X There is a 1.8% of reference with a coverageData >= 2X There is a 1.44% of reference with a coverageData >= 3X There is a 1.23% of reference with a coverageData >= 4X There is a 1.09% of reference with a coverageData >= 5X There is a 0.98% of reference with a coverageData >= 6X There is a 0.9% of reference with a coverageData >= 7X There is a 0.83% of reference with a coverageData >= 8X There is a 0.77% of reference with a coverageData >= 9X There is a 0.73% of reference with a coverageData >= 10X There is a 0.68% of reference with a coverageData >= 11X There is a 0.64% of reference with a coverageData >= 12X There is a 0.61% of reference with a coverageData >= 13X There is a 0.58% of reference with a coverageData >= 14X There is a 0.55% of reference with a coverageData >= 15X There is a 0.53% of reference with a coverageData >= 16X There is a 0.5% of reference with a coverageData >= 17X There is a 0.48% of reference with a coverageData >= 18X There is a 0.46% of reference with a coverageData >= 19X There is a 0.45% of reference with a coverageData >= 20X There is a 0.43% of reference with a coverageData >= 21X There is a 0.41% of reference with a coverageData >= 22X There is a 0.4% of reference with a coverageData >= 23X There is a 0.39% of reference with a coverageData >= 24X There is a 0.37% of reference with a coverageData >= 25X There is a 0.36% of reference with a coverageData >= 26X There is a 0.35% of reference with a coverageData >= 27X There is a 0.34% of reference with a coverageData >= 28X There is a 0.33% of reference with a coverageData >= 29X There is a 0.32% of reference with a coverageData >= 30X There is a 0.31% of reference with a coverageData >= 31X There is a 0.3% of reference with a coverageData >= 32X There is a 0.29% of reference with a coverageData >= 33X There is a 0.28% of reference with a coverageData >= 34X There is a 0.28% of reference with a coverageData >= 35X There is a 0.27% of reference with a coverageData >= 36X There is a 0.26% of reference with a coverageData >= 37X There is a 0.26% of reference with a coverageData >= 38X There is a 0.25% of reference with a coverageData >= 39X There is a 0.24% of reference with a coverageData >= 40X There is a 0.24% of reference with a coverageData >= 41X There is a 0.23% of reference with a coverageData >= 42X There is a 0.23% of reference with a coverageData >= 43X There is a 0.22% of reference with a coverageData >= 44X There is a 0.22% of reference with a coverageData >= 45X There is a 0.21% of reference with a coverageData >= 46X There is a 0.21% of reference with a coverageData >= 47X There is a 0.2% of reference with a coverageData >= 48X There is a 0.2% of reference with a coverageData >= 49X There is a 0.2% of reference with a coverageData >= 50X There is a 0.19% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 86581169 0.3473659108757045 10.23188993862173 chr2 243199373 119230603 0.49025867759946895 12.21701916734315 chr3 198022430 67454972 0.34064308775526086 7.549034728612488 chr4 191154276 121080376 0.6334170416360448 9.448383502736052 chr5 180915260 93199731 0.5151568253556942 15.03004348378878 chr6 171115067 105259300 0.6151375319860056 28.95557129899434 chr7 159138663 88444268 0.5557685752330344 49.138994601733614 chr8 146364022 71421153 0.4879693248659155 10.01444530683018 chr9 141213431 108959730 0.7715960813954021 18.12679585432482 chr10 135534747 75806832 0.5593165861740237 17.741281167536155 chr11 135006516 55293368 0.4095607355722001 9.362108939967822 chr12 133851895 78182716 0.5840986860888298 12.04624871045858 chr13 115169878 61477153 0.5337954165411203 10.168388326244015 chr14 107349540 60350939 0.5621909418521961 10.093286916893184 chr15 102531392 34261361 0.3341548410851576 8.659843450120267 chr16 90354753 30161984 0.33381734771606314 42.309201606934614 chr17 81195210 21940161 0.2702149671144394 5.773027294871312 chr18 78077248 25519462 0.32684889201012823 7.1433739369639095 chr19 59128983 33650755 0.5691076235828375 78.98820739095503 chr20 63025520 11213251 0.17791604099418776 5.853082170692098 chr21 48129895 9122473 0.18953860173598966 4.3629982552349045 chr22 51304566 3715038 0.07241144969436053 3.1660990791387196 chrMT 16571 50700812 3059.6108864884436 3387.262816338703 chrX 155270560 60322831 0.3885014068346247 7.139285904188492 chrY 59373566 10967689 0.18472343399417848 4.6925145254090985