BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714163.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 = 810,002 number of mapped reads = 674,125 (83.23%) number of supplementary alignments = 19,114 (2.36%) number of secondary alignments = 0 number of mapped bases = 87,656,811 bp number of sequenced bases = 85,742,908 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 611,191 duplication rate = 44.61% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.3995 >>>>>>> ACTG content number of A's = 22,643,616 bp (26.41%) number of C's = 19,258,790 bp (22.46%) number of T's = 21,481,608 bp (25.05%) number of G's = 22,358,309 bp (26.08%) number of N's = 585 bp (0%) GC percentage = 48.54% >>>>>>> Mismatches and indels general error rate = 0.0437 number of mismatches = 3,495,084 number of insertions = 89,473 mapped reads with insertion percentage = 12.75% number of deletions = 303,022 mapped reads with deletion percentage = 42.68% homopolymer indels = 30.1% >>>>>>> Coverage mean coverageData = 0.0283X std coverageData = 8.0988X There is a 0.06% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 8145576 0.03268026361306438 8.990978483817088 chr2 243199373 10929528 0.04494060928356094 13.949080382281425 chr3 198022430 2948764 0.014891060573289601 3.5300633079224384 chr4 191154276 2699546 0.014122341683844937 2.780328625280389 chr5 180915260 4203388 0.023234015748588594 4.777119881064789 chr6 171115067 2975332 0.0173879019081353 3.741158566176482 chr7 159138663 2551580 0.01603369006562535 2.6839526812208048 chr8 146364022 2907168 0.019862586175720152 4.203158425757916 chr9 141213431 3493195 0.024736988367629137 5.300577729847364 chr10 135534747 3786487 0.027937389369236804 4.1092260602001165 chr11 135006516 4468803 0.033100646786559544 5.350619281322724 chr12 133851895 5522677 0.04125961010862043 12.345130197021835 chr13 115169878 3392167 0.02945359549655857 9.09443159139064 chr14 107349540 5265598 0.04905096006932121 24.015816546247226 chr15 102531392 3275757 0.031948820123304286 5.695125218826249 chr16 90354753 1528016 0.016911296298934047 2.2879213078893477 chr17 81195210 3134349 0.038602634317960384 6.473203406803881 chr18 78077248 2412116 0.030893967984117473 6.387696530104935 chr19 59128983 2398390 0.04056200323959572 4.71750245992167 chr20 63025520 2576755 0.0408843116248783 6.252464289453355 chr21 48129895 1065594 0.022139961036690397 4.255517377926707 chr22 51304566 554318 0.010804457443417414 1.1669317927797658 chrMT 16571 109121 6.585058234264679 51.6747693052021 chrX 155270560 6692482 0.04310206648317621 5.107549461023043 chrY 59373566 620104 0.010444109083830337 1.8921862590146827