BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080917.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 = 5,006,797 number of mapped reads = 4,516,593 (90.21%) number of supplementary alignments = 56,342 (1.13%) number of secondary alignments = 0 number of mapped bases = 312,071,647 bp number of sequenced bases = 311,955,290 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 245,763 duplication rate = 4.18% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.7025 >>>>>>> ACTG content number of A's = 89,696,743 bp (28.75%) number of C's = 56,381,526 bp (18.07%) number of T's = 98,609,763 bp (31.61%) number of G's = 65,754,863 bp (21.08%) number of N's = 1,512,395 bp (0.48%) GC percentage = 39.15% >>>>>>> Mismatches and indels general error rate = 0.0116 number of mismatches = 3,565,651 number of insertions = 23,697 mapped reads with insertion percentage = 0.52% number of deletions = 70,090 mapped reads with deletion percentage = 1.54% homopolymer indels = 49.65% >>>>>>> Coverage mean coverageData = 0.1008X std coverageData = 0.707X There is a 6.98% of reference with a coverageData >= 1X There is a 2% of reference with a coverageData >= 2X There is a 0.62% of reference with a coverageData >= 3X There is a 0.2% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 22178430 0.08898044029346672 1.2111755720184936 chr2 243199373 28096410 0.11552829949113397 0.7140533798148517 chr3 198022430 20950857 0.1058004237196766 0.4363073980092497 chr4 191154276 20440965 0.10693438529201409 0.4733155041681883 chr5 180915260 21340534 0.11795872830185801 0.46317006941707795 chr6 171115067 20720599 0.12109161024376655 0.7302816935704544 chr7 159138663 15045832 0.09454542168674623 0.9211680690508227 chr8 146364022 17153915 0.11720035269323222 1.158307219152547 chr9 141213431 13122721 0.09292827818906263 0.6254127235522509 chr10 135534747 14055530 0.10370425526378117 0.6822308661467289 chr11 135006516 13600718 0.10074119681749287 0.6308008894891367 chr12 133851895 13786518 0.10299830271360745 0.43547376341085053 chr13 115169878 10775696 0.09356349235691645 0.4115373823765091 chr14 107349540 8900864 0.08291478473033047 0.4038990400513066 chr15 102531392 9605700 0.09368545391444602 0.41051741475590137 chr16 90354753 7852662 0.08690922988854831 0.4349950797266397 chr17 81195210 7904355 0.09735001609085069 0.517928850542092 chr18 78077248 8509505 0.10898828042709702 1.155059562732719 chr19 59128983 4220915 0.07138487397965225 0.8742915445269198 chr20 63025520 6805221 0.10797564224777519 0.45782590560956665 chr21 48129895 3266127 0.06786067162623147 0.3925687851446842 chr22 51304566 2845702 0.05546683700628127 0.3091478561159141 chrMT 16571 44597 2.6912678776175247 2.23254805630128 chrX 155270560 20112600 0.12953260424899607 0.5384806509724034 chrY 59373566 734674 0.012373755687842634 0.2527149581074646