BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714049.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 = 462,682 number of mapped reads = 73,776 (15.95%) number of supplementary alignments = 1,389 (0.3%) number of secondary alignments = 0 number of mapped bases = 7,585,620 bp number of sequenced bases = 7,569,866 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 72,645 duplication rate = 36.9% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 12.8842 >>>>>>> ACTG content number of A's = 153,004 bp (2.02%) number of C's = 64,444 bp (0.85%) number of T's = 81,369 bp (1.07%) number of G's = 7,270,904 bp (96.05%) number of N's = 145 bp (0%) GC percentage = 96.9% >>>>>>> Mismatches and indels general error rate = 0.0326 number of mismatches = 187,261 number of insertions = 8,652 mapped reads with insertion percentage = 8.11% number of deletions = 3,540 mapped reads with deletion percentage = 4.62% homopolymer indels = 63.05% >>>>>>> Coverage mean coverageData = 0.0025X std coverageData = 9.323X 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 25456 1.0213013671889708E-4 0.16496939935452756 chr2 243199373 7298282 0.0300094605918248 33.26106211974748 chr3 198022430 8150 4.1156953785487835E-5 0.01523990907784355 chr4 191154276 8232 4.306469189315964E-5 0.018280835605766658 chr5 180915260 7605 4.203625498479233E-5 0.012780022469452463 chr6 171115067 10035 5.864474809807368E-5 0.021807061242400547 chr7 159138663 15198 9.550161923881439E-5 0.11007266077999314 chr8 146364022 14057 9.604136185872236E-5 0.041085043142301984 chr9 141213431 6627 4.6928963860385205E-5 0.015053882597462606 chr10 135534747 23559 1.7382258440339288E-4 0.21129437135381374 chr11 135006516 6039 4.473117430865337E-5 0.026459076518231518 chr12 133851895 9844 7.354397186532174E-5 0.04929451347984143 chr13 115169878 1219 1.0584364776352372E-5 0.003619706101272076 chr14 107349540 13544 1.261672849273504E-4 0.13171560742652488 chr15 102531392 7376 7.19389433433226E-5 0.021221565351420515 chr16 90354753 4131 4.571978631826928E-5 0.01245382333753828 chr17 81195210 13181 1.6233716250010314E-4 0.1165881442581936 chr18 78077248 2841 3.638704069077845E-5 0.02521745759347008 chr19 59128983 2945 4.980636991507194E-5 0.01575599595784932 chr20 63025520 4711 7.474749910829772E-5 0.025210362039816487 chr21 48129895 1353 2.8111426380631E-5 0.009592758900280274 chr22 51304566 2437 4.7500645459119566E-5 0.01443269876944222 chrMT 16571 1636 0.09872669120753123 0.5698181501392688 chrX 155270560 93843 6.043837286347135E-4 0.08969357521048112 chrY 59373566 3319 5.590029744886807E-5 0.012371127864010659