BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081141.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 = 2,709,122 number of mapped reads = 2,412,135 (89.04%) number of supplementary alignments = 23,137 (0.85%) number of secondary alignments = 0 number of mapped bases = 161,536,520 bp number of sequenced bases = 161,478,419 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 101,390 duplication rate = 3.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7452 >>>>>>> ACTG content number of A's = 45,468,803 bp (28.16%) number of C's = 30,190,696 bp (18.7%) number of T's = 50,372,403 bp (31.19%) number of G's = 35,398,534 bp (21.92%) number of N's = 47,983 bp (0.03%) GC percentage = 40.62% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,335,251 number of insertions = 11,951 mapped reads with insertion percentage = 0.49% number of deletions = 36,362 mapped reads with deletion percentage = 1.49% homopolymer indels = 47.17% >>>>>>> Coverage mean coverageData = 0.0522X std coverageData = 0.3904X There is a 4.44% of reference with a coverageData >= 1X There is a 0.58% of reference with a coverageData >= 2X There is a 0.09% 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 11667045 0.04680848919529874 0.6514471365385274 chr2 243199373 14331273 0.058928083667386756 0.48352238106607964 chr3 198022430 12111715 0.061163349020613475 0.2789094237631173 chr4 191154276 11018441 0.05764161404372665 0.27950576784402775 chr5 180915260 9476645 0.05238167858255849 0.26063427441692044 chr6 171115067 9794094 0.05723688843835125 0.33226304331680684 chr7 159138663 9427067 0.05923806837562787 0.48934207168753574 chr8 146364022 6768922 0.046247171316459175 0.47952738971181674 chr9 141213431 6509235 0.04609501344103735 0.37180053603081126 chr10 135534747 7923085 0.058457961337397855 0.34886602827057456 chr11 135006516 8014415 0.059363171774612714 0.4093896867722291 chr12 133851895 7584442 0.05666294078242225 0.27509337926698596 chr13 115169878 4980210 0.04324229639281202 0.23563577176407907 chr14 107349540 4103991 0.03823016847580343 0.241708385353667 chr15 102531392 4797992 0.046795346346219506 0.25216002934726706 chr16 90354753 4468185 0.049451576720042606 0.2748482677564878 chr17 81195210 3685773 0.045393970900500166 0.2795170186327942 chr18 78077248 4355734 0.0557874939444587 0.6538360555818101 chr19 59128983 2884013 0.04877494679724155 0.4760710946166399 chr20 63025520 3657009 0.058024257475384575 0.2815802873236677 chr21 48129895 1854833 0.038538064543876524 0.24107577284782786 chr22 51304566 1474782 0.028745628605453946 0.1897258258474868 chrMT 16571 2481 0.14971938929455073 0.4042160733425595 chrX 155270560 10292409 0.06628693166302743 0.33322883793082536 chrY 59373566 352729 0.005940842428093337 0.11461314618476162