BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080719.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 = 2,313,273 number of mapped reads = 2,086,923 (90.22%) number of supplementary alignments = 12,378 (0.54%) number of secondary alignments = 0 number of mapped bases = 141,671,294 bp number of sequenced bases = 141,619,253 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 113,360 duplication rate = 4.48% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4989 >>>>>>> ACTG content number of A's = 39,833,656 bp (28.13%) number of C's = 26,180,486 bp (18.49%) number of T's = 45,030,459 bp (31.8%) number of G's = 30,572,555 bp (21.59%) number of N's = 2,097 bp (0%) GC percentage = 40.07% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,149,473 number of insertions = 10,282 mapped reads with insertion percentage = 0.49% number of deletions = 29,266 mapped reads with deletion percentage = 1.39% homopolymer indels = 47.85% >>>>>>> Coverage mean coverageData = 0.0458X std coverageData = 0.4183X There is a 3.78% of reference with a coverageData >= 1X There is a 0.59% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 16881421 0.06772870186750708 0.5968524991025661 chr2 243199373 9482664 0.03899131762975392 0.3978472981301863 chr3 198022430 8789079 0.04438425990429468 0.2444349241496889 chr4 191154276 6272692 0.03281481393594355 0.22069142033599773 chr5 180915260 6470356 0.035764567344954756 0.2193272165891662 chr6 171115067 8489619 0.04961350948715697 0.36134052302424746 chr7 159138663 9173834 0.05764679573812933 1.1098896706493604 chr8 146364022 17071038 0.11663411381247776 0.555442505541699 chr9 141213431 4464080 0.03161229047681732 0.28515277401626893 chr10 135534747 6812650 0.05026497005967038 0.36363293331346147 chr11 135006516 5893152 0.043650870895742544 0.28232681984380703 chr12 133851895 4498073 0.0336048510930682 0.21591136485974322 chr13 115169878 2994360 0.025999506572369557 0.18551867603040334 chr14 107349540 2766774 0.02577350587622453 0.19574943598582356 chr15 102531392 2506355 0.024444757367577726 0.18046116922529867 chr16 90354753 3500431 0.03874097248652763 0.24804459677286989 chr17 81195210 2223201 0.027380937865669662 0.20027629047580034 chr18 78077248 4086379 0.05233764130620997 0.4743518231296737 chr19 59128983 2296859 0.03884489269839125 0.39338886185532435 chr20 63025520 3520806 0.05586318050212041 0.2792887511616217 chr21 48129895 2169464 0.04507518663815909 0.25687064197046916 chr22 51304566 1350086 0.02631512368704181 0.18604912343036006 chrMT 16571 61560 3.71492366181884 2.8423423237877747 chrX 155270560 9566906 0.06161442323644611 0.31264716204961074 chrY 59373566 329455 0.005548849802957768 0.12187158568646067