BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230385.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 = 2,552,555 number of mapped reads = 2,130,047 (83.45%) number of supplementary alignments = 14,132 (0.55%) number of secondary alignments = 0 number of mapped bases = 139,502,851 bp number of sequenced bases = 139,439,794 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 101,753 duplication rate = 3.75% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.881 >>>>>>> ACTG content number of A's = 37,876,339 bp (27.16%) number of C's = 24,347,797 bp (17.46%) number of T's = 45,774,350 bp (32.83%) number of G's = 31,174,821 bp (22.36%) number of N's = 266,487 bp (0.19%) GC percentage = 39.82% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 1,285,296 number of insertions = 12,524 mapped reads with insertion percentage = 0.58% number of deletions = 37,838 mapped reads with deletion percentage = 1.76% homopolymer indels = 48.1% >>>>>>> Coverage mean coverageData = 0.0451X std coverageData = 0.3997X There is a 3.78% of reference with a coverageData >= 1X There is a 0.53% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 10713829 0.04298416171247975 0.7377631685505772 chr2 243199373 11985824 0.04928394284963884 0.41626188822635357 chr3 198022430 10058391 0.05079420043476893 0.26087610545435647 chr4 191154276 9126667 0.04774503187153396 0.2722787722294081 chr5 180915260 8619551 0.04764413460755052 0.25160680701845756 chr6 171115067 9051468 0.052896966694347264 0.32284810885126275 chr7 159138663 6666980 0.04189415616744248 0.4108967859471828 chr8 146364022 8014624 0.05475815634527999 0.6426814179576739 chr9 141213431 5730005 0.04057691226268697 0.39540693623372614 chr10 135534747 7299925 0.05386017358338375 0.3945173780497798 chr11 135006516 6723884 0.04980414426811814 0.3677417779259277 chr12 133851895 6625335 0.04949750618024496 0.2596071547322056 chr13 115169878 5078018 0.044091546228780414 0.2398654255498957 chr14 107349540 4689714 0.043686391203912 0.25376618288119807 chr15 102531392 4046467 0.03946563994761721 0.2280116275613755 chr16 90354753 4082607 0.04518419744891561 0.2775701615067897 chr17 81195210 3464930 0.0426740690737791 0.26955563952804035 chr18 78077248 4089107 0.05237258106228334 0.6775751399930121 chr19 59128983 2499814 0.04227730417754691 0.49829525141737296 chr20 63025520 2833359 0.04495574173763263 0.2552663397925939 chr21 48129895 1980709 0.041153403721325386 0.255243026318262 chr22 51304566 1487776 0.0289989004097608 0.1946358217880269 chrMT 16571 110505 6.668577635628508 4.188298958569349 chrX 155270560 4185487 0.026956088778194654 0.2240114334405596 chrY 59373566 337875 0.005690663754304399 0.16246839487969972