BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714068.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 11,786 number of mapped reads = 8,159 (69.23%) number of supplementary alignments = 149 (1.26%) number of secondary alignments = 0 number of mapped bases = 1,045,032 bp number of sequenced bases = 1,022,017 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,422 duplication rate = 37.27% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 27.5421 >>>>>>> ACTG content number of A's = 281,558 bp (27.55%) number of C's = 201,853 bp (19.75%) number of T's = 266,906 bp (26.12%) number of G's = 271,692 bp (26.58%) number of N's = 8 bp (0%) GC percentage = 46.33% >>>>>>> Mismatches and indels general error rate = 0.0459 number of mismatches = 42,996 number of insertions = 1,251 mapped reads with insertion percentage = 14.95% number of deletions = 3,930 mapped reads with deletion percentage = 44.98% homopolymer indels = 30.13% >>>>>>> Coverage mean coverageData = 0.0003X std coverageData = 0.157X There is a 0% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% 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 100093 4.015757296749122E-4 0.14005162422687878 chr2 243199373 151908 6.24623320883315E-4 0.3358439349056224 chr3 198022430 70916 3.581210471965221E-4 0.12100173167909979 chr4 191154276 47089 2.463402911269429E-4 0.10194335783879965 chr5 180915260 70089 3.874134221734529E-4 0.1310057714999966 chr6 171115067 58353 3.410161420794114E-4 0.18222857721367583 chr7 159138663 27456 1.7252878390715146E-4 0.09345466967705773 chr8 146364022 27223 1.859951621170946E-4 0.12030093400272245 chr9 141213431 29389 2.081175975392879E-4 0.0836732466860938 chr10 135534747 37462 2.7640144560125236E-4 0.1068591345351265 chr11 135006516 58595 4.3401608852716413E-4 0.14049352578479746 chr12 133851895 49423 3.6923646094065386E-4 0.13888885646066673 chr13 115169878 29724 2.580883171552895E-4 0.16343264340018115 chr14 107349540 40009 3.726983832441201E-4 0.13895942306780115 chr15 102531392 17828 1.7387845470780304E-4 0.0809125046668257 chr16 90354753 23517 2.602740776680558E-4 0.13118866252576372 chr17 81195210 45095 5.553899053897391E-4 0.20049742230113718 chr18 78077248 37935 4.8586497310970796E-4 0.1669503986039432 chr19 59128983 1968 3.328317011642159E-5 0.014486035375196353 chr20 63025520 33942 5.385437518008578E-4 0.19777556015959016 chr21 48129895 8038 1.6700638968773982E-4 0.07660401783202189 chr22 51304566 1063 2.0719403415282763E-5 0.011575135229463698 chrMT 16571 5243 0.3163961136925955 1.8018774010099938 chrX 155270560 72610 4.676353328023033E-4 0.14708266368056014 chrY 59373566 64 1.077920770330689E-6 0.0010382290731902578