BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080653.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 1,216,468 number of mapped reads = 1,116,066 (91.75%) number of supplementary alignments = 8,961 (0.74%) number of secondary alignments = 0 number of mapped bases = 74,949,278 bp number of sequenced bases = 74,920,134 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 31,686 duplication rate = 2.5% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0902 >>>>>>> ACTG content number of A's = 20,857,011 bp (27.84%) number of C's = 13,738,178 bp (18.34%) number of T's = 23,742,753 bp (31.69%) number of G's = 16,578,894 bp (22.13%) number of N's = 3,298 bp (0%) GC percentage = 40.47% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 509,947 number of insertions = 5,815 mapped reads with insertion percentage = 0.52% number of deletions = 17,663 mapped reads with deletion percentage = 1.57% homopolymer indels = 48.82% >>>>>>> Coverage mean coverageData = 0.0242X std coverageData = 0.1958X There is a 2.17% of reference with a coverageData >= 1X There is a 0.21% of reference with a coverageData >= 2X There is a 0.03% 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 9197403 0.036900221002859605 0.23510081753342005 chr2 243199373 5123187 0.021065790329977536 0.25748953013582365 chr3 198022430 4677038 0.023618728444045455 0.16734890937612978 chr4 191154276 3212909 0.016807936852011617 0.14279188806902113 chr5 180915260 3404783 0.018819766779209227 0.14896949638385337 chr6 171115067 4537905 0.02651961092356642 0.199599156899924 chr7 159138663 4616582 0.029009807629212018 0.3071243238746663 chr8 146364022 8934549 0.0610433416485371 0.29267143109395094 chr9 141213431 2288189 0.016203763224193597 0.15374084529116458 chr10 135534747 3526499 0.026019150646291463 0.18296748004391544 chr11 135006516 3075031 0.02277690804197925 0.17137535631115428 chr12 133851895 2448174 0.018290170639720865 0.14830881598103493 chr13 115169878 1565376 0.013591887281499074 0.12751987648165264 chr14 107349540 1422938 0.013255184884816461 0.12619951509624988 chr15 102531392 1307591 0.012753079564159239 0.12556096914870743 chr16 90354753 1845096 0.020420574886636015 0.15928877363335017 chr17 81195210 1186868 0.014617463271540279 0.13172711973672882 chr18 78077248 2509900 0.03214636868348639 0.23369230527890203 chr19 59128983 1181431 0.019980573655393328 0.16854801158927113 chr20 63025520 1912507 0.03034496185037426 0.19093295431616364 chr21 48129895 1142159 0.023730760268643843 0.1705051620456812 chr22 51304566 714233 0.013921431476488857 0.12757007730314715 chrMT 16571 19684 1.1878583066803452 1.3329320800303017 chrX 155270560 4953702 0.03190367832768813 0.2003877140256839 chrY 59373566 145544 0.002451326571828278 0.055987706690829316