BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085022.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 = 2,427,293 number of mapped reads = 2,165,751 (89.22%) number of supplementary alignments = 13,786 (0.57%) number of secondary alignments = 0 number of mapped bases = 142,114,729 bp number of sequenced bases = 142,065,463 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 71,378 duplication rate = 2.51% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.1492 >>>>>>> ACTG content number of A's = 38,733,793 bp (27.26%) number of C's = 27,534,560 bp (19.38%) number of T's = 43,006,039 bp (30.27%) number of G's = 32,785,684 bp (23.08%) number of N's = 5,387 bp (0%) GC percentage = 42.46% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 1,247,413 number of insertions = 10,090 mapped reads with insertion percentage = 0.46% number of deletions = 28,813 mapped reads with deletion percentage = 1.32% homopolymer indels = 45.87% >>>>>>> Coverage mean coverageData = 0.0459X std coverageData = 0.3633X There is a 3.97% of reference with a coverageData >= 1X There is a 0.45% of reference with a coverageData >= 2X There is a 0.07% 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% 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 12421183 0.04983411054370051 0.5615588178433029 chr2 243199373 13787179 0.0566908492810958 0.4950094040972248 chr3 198022430 8583298 0.04334507964577548 0.23578784766059416 chr4 191154276 8170583 0.04274339643859183 0.2379704030369401 chr5 180915260 7096732 0.03922682917958386 0.2223576365458286 chr6 171115067 9792973 0.05723033729110482 0.35411027160033787 chr7 159138663 12633239 0.07938510203519807 0.4220410694549665 chr8 146364022 8329195 0.05690739353965007 0.547521723756147 chr9 141213431 4665464 0.03303838712055654 0.34004131718133856 chr10 135534747 10278329 0.07583537969049368 0.48942416662557336 chr11 135006516 5576108 0.04130251016921287 0.32466405776923446 chr12 133851895 5938897 0.044369166383486765 0.24287143865177946 chr13 115169878 2717067 0.023591819729113544 0.1699356048179318 chr14 107349540 4706646 0.04384411894079844 0.25105689280496657 chr15 102531392 2515056 0.0245296191823866 0.19339079534977607 chr16 90354753 3992962 0.044192052630590443 0.25303721094060483 chr17 81195210 2429918 0.029926863912292365 0.21445844242906 chr18 78077248 3400636 0.04355476258589442 0.5341533916279704 chr19 59128983 2522836 0.042666656384061266 0.40842529740107114 chr20 63025520 3308432 0.05249352960515042 0.262946940194616 chr21 48129895 1575579 0.03273597417987303 0.2174442899873495 chr22 51304566 1011809 0.019721616980445757 0.1559682915357528 chrMT 16571 10049 0.6064208557117856 0.911220849346684 chrX 155270560 6353233 0.04091717708753031 0.25688607108459444 chrY 59373566 297326 0.005007716733739725 0.10151009324244548