BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472819.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 2,722,878 number of mapped reads = 2,256,717 (82.88%) number of supplementary alignments = 17,056 (0.63%) number of secondary alignments = 0 number of mapped bases = 147,363,745 bp number of sequenced bases = 147,302,308 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 69,755 duplication rate = 2.36% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2099 >>>>>>> ACTG content number of A's = 39,626,776 bp (26.9%) number of C's = 29,493,271 bp (20.02%) number of T's = 43,664,177 bp (29.64%) number of G's = 34,515,096 bp (23.43%) number of N's = 2,988 bp (0%) GC percentage = 43.45% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,245,409 number of insertions = 11,360 mapped reads with insertion percentage = 0.5% number of deletions = 34,073 mapped reads with deletion percentage = 1.49% homopolymer indels = 45.26% >>>>>>> Coverage mean coverageData = 0.0476X std coverageData = 0.3351X There is a 4.1% of reference with a coverageData >= 1X There is a 0.49% of reference with a coverageData >= 2X There is a 0.08% 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 12497280 0.05013941369478073 0.40112377347170697 chr2 243199373 14223701 0.058485763448082574 0.47742266533644806 chr3 198022430 8847998 0.04468179690553237 0.23659780466833102 chr4 191154276 6723474 0.03517302432721934 0.24454469908825133 chr5 180915260 8529212 0.047144790328908684 0.24381440417155015 chr6 171115067 10454229 0.06109473106772065 0.3011114028361033 chr7 159138663 8078590 0.05076447073078652 0.41413644380226156 chr8 146364022 10434578 0.07129195998727064 0.3928183599644602 chr9 141213431 6228467 0.0441067606380869 0.3547883908359286 chr10 135534747 7001337 0.05165713704397884 0.326979721047012 chr11 135006516 5583353 0.04135617424569345 0.34447299953527405 chr12 133851895 5271410 0.039382408444796395 0.22883555525701027 chr13 115169878 6702991 0.058200903885649684 0.2798735122805814 chr14 107349540 3443058 0.0320733372495122 0.23400506432771281 chr15 102531392 3170301 0.030920296098194005 0.21158181844790774 chr16 90354753 4517271 0.04999483535747146 0.27336763433082945 chr17 81195210 3785033 0.04661645680822797 0.2674463870148593 chr18 78077248 2806160 0.03594081594679157 0.6399362861960418 chr19 59128983 3175123 0.05369825149876161 0.34705906224174277 chr20 63025520 5038700 0.07994698020738265 0.33324034464355584 chr21 48129895 2390589 0.04966952452316798 0.3081459485674038 chr22 51304566 1587109 0.030935043871143944 0.2090599245710598 chrMT 16571 78867 4.759338603584576 3.5912385860566918 chrX 155270560 6042220 0.038914138005298624 0.2586885390457498 chrY 59373566 752694 0.012677257754738868 0.16763747511825874