BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008735.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 = 1,589,685 number of mapped reads = 831,623 (52.31%) number of supplementary alignments = 3,148 (0.2%) number of secondary alignments = 0 number of mapped bases = 51,899,504 bp number of sequenced bases = 51,868,732 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 34,265 duplication rate = 3.03% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6126 >>>>>>> ACTG content number of A's = 14,635,938 bp (28.22%) number of C's = 8,692,071 bp (16.76%) number of T's = 15,888,178 bp (30.63%) number of G's = 12,650,286 bp (24.39%) number of N's = 2,259 bp (0%) GC percentage = 41.15% >>>>>>> Mismatches and indels general error rate = 0.0099 number of mismatches = 506,489 number of insertions = 4,405 mapped reads with insertion percentage = 0.53% number of deletions = 20,147 mapped reads with deletion percentage = 2.39% homopolymer indels = 48.85% >>>>>>> Coverage mean coverageData = 0.0168X std coverageData = 0.1782X There is a 1.5% of reference with a coverageData >= 1X There is a 0.12% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 4020801 0.016131558605023497 0.20153475842202215 chr2 243199373 4555140 0.01873006473581657 0.2387093916575033 chr3 198022430 3793557 0.019157208605106 0.15930118572694324 chr4 191154276 3121227 0.01632831378566703 0.14567069099475605 chr5 180915260 2504285 0.013842309377329474 0.1343438063117472 chr6 171115067 2943164 0.01719991144906018 0.15955268975735837 chr7 159138663 3823269 0.02402476511946063 0.28038499977908954 chr8 146364022 3366798 0.023002907094203794 0.2183573002146469 chr9 141213431 1988729 0.014083143408646448 0.16327530127813972 chr10 135534747 2521075 0.018600949614787712 0.16715952121736266 chr11 135006516 2009618 0.014885340793476962 0.17027479055427408 chr12 133851895 2362932 0.017653332438812317 0.15325646084786762 chr13 115169878 2050922 0.017807798667634257 0.15239694657698613 chr14 107349540 1707348 0.01590456745320008 0.14663262430923513 chr15 102531392 1378498 0.013444643373221736 0.134837851062219 chr16 90354753 1243153 0.013758578920579861 0.13847010147848743 chr17 81195210 1363592 0.01679399560639107 0.1534616761608422 chr18 78077248 1098961 0.014075303986124102 0.23558857533151153 chr19 59128983 926075 0.01566194703534813 0.16281518363706107 chr20 63025520 1146801 0.01819581972508914 0.15266500753649903 chr21 48129895 592760 0.012315838212404161 0.12666966613758196 chr22 51304566 495101 0.009650232690790133 0.1107947187102344 chrMT 16571 23283 1.40504495805926 2.165825511595276 chrX 155270560 2731626 0.017592684666043582 0.1578790584700246 chrY 59373566 130789 0.002202815306730945 0.057393344441608596