BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714245.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 = 348,262 number of mapped reads = 49,661 (14.26%) number of supplementary alignments = 1,484 (0.43%) number of secondary alignments = 0 number of mapped bases = 4,901,195 bp number of sequenced bases = 4,886,734 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 48,579 duplication rate = 34.37% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 12.6352 >>>>>>> ACTG content number of A's = 179,663 bp (3.68%) number of C's = 87,821 bp (1.8%) number of T's = 116,500 bp (2.38%) number of G's = 4,502,601 bp (92.14%) number of N's = 149 bp (0%) GC percentage = 93.94% >>>>>>> Mismatches and indels general error rate = 0.0337 number of mismatches = 122,999 number of insertions = 5,981 mapped reads with insertion percentage = 8.1% number of deletions = 2,902 mapped reads with deletion percentage = 5.49% homopolymer indels = 60.36% >>>>>>> Coverage mean coverageData = 0.0016X std coverageData = 5.6327X 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 65872 2.6428018408026355E-4 0.43109936297490126 chr2 243199373 4483799 0.018436721051908304 20.087077283012416 chr3 198022430 6234 3.1481282196163334E-5 0.011013326024635109 chr4 191154276 16635 8.702394917914366E-5 0.03512656563405161 chr5 180915260 5954 3.291043552655536E-5 0.012400729955709488 chr6 171115067 9196 5.374161469954016E-5 0.019323430734105498 chr7 159138663 11932 7.497863671256306E-5 0.06832937724002436 chr8 146364022 12086 8.25749377124933E-5 0.028116839297071282 chr9 141213431 3700 2.6201473711094804E-5 0.010682904013505402 chr10 135534747 40105 2.9590198002878187E-4 0.5033640572573798 chr11 135006516 8514 6.306362279580638E-5 0.034766905021668335 chr12 133851895 9474 7.077972261804736E-5 0.05014722928747783 chr13 115169878 2727 2.3678066238812896E-5 0.007176766587042492 chr14 107349540 13477 1.2554315556452314E-4 0.07379434994103695 chr15 102531392 4274 4.168479444812375E-5 0.015101499138191608 chr16 90354753 8773 9.709505818692238E-5 0.03240194218390843 chr17 81195210 10781 1.327787685997733E-4 0.09645433035543537 chr18 78077248 2630 3.3684588883050794E-5 0.0151074281154113 chr19 59128983 7009 1.1853746917987749E-4 0.03949896677692963 chr20 63025520 6413 1.0175243298270288E-4 0.030664687002602577 chr21 48129895 8518 1.7697940126401687E-4 0.08139026600874315 chr22 51304566 968 1.886771637440613E-5 0.01326383827578317 chrMT 16571 232 0.014000362078329612 0.22009811177340288 chrX 155270560 151275 9.742671115503158E-4 0.165295088705014 chrY 59373566 10617 1.7881695029063944E-4 0.04270194739453658