BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084261.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 = 2,784,822 number of mapped reads = 1,666,983 (59.86%) number of supplementary alignments = 7,238 (0.26%) number of secondary alignments = 0 number of mapped bases = 101,788,307 bp number of sequenced bases = 101,755,402 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 51,313 duplication rate = 2.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1616 >>>>>>> ACTG content number of A's = 29,027,020 bp (28.53%) number of C's = 19,874,231 bp (19.53%) number of T's = 30,173,843 bp (29.65%) number of G's = 22,679,179 bp (22.29%) number of N's = 1,129 bp (0%) GC percentage = 41.82% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 823,699 number of insertions = 7,189 mapped reads with insertion percentage = 0.43% number of deletions = 20,532 mapped reads with deletion percentage = 1.22% homopolymer indels = 45.56% >>>>>>> Coverage mean coverageData = 0.0329X std coverageData = 0.2591X There is a 2.95% of reference with a coverageData >= 1X There is a 0.26% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 8012382 0.03214588580704078 0.3677842658332193 chr2 243199373 8399278 0.034536593973866866 0.3182286530540885 chr3 198022430 7073074 0.03571854966126817 0.20552957946468953 chr4 191154276 6826898 0.03571407421720454 0.21308864508110803 chr5 180915260 6479023 0.03581247375152323 0.20573470033175834 chr6 171115067 6129383 0.03582024135840709 0.2323165645637676 chr7 159138663 5569143 0.03499553719387475 0.34166813015159353 chr8 146364022 5077135 0.03468840860358429 0.26397664559125306 chr9 141213431 4281499 0.030319346889886134 0.25064245765129267 chr10 135534747 4637661 0.03421750586216832 0.2535961348357272 chr11 135006516 4474338 0.03314164480772173 0.23221615785050942 chr12 133851895 4740080 0.03541287181627126 0.2070030323888404 chr13 115169878 3178720 0.02760027235593668 0.18078182847723795 chr14 107349540 3048502 0.028397904639367807 0.19532093473451584 chr15 102531392 2915107 0.028431360807039466 0.18954219353721002 chr16 90354753 2858414 0.03163545807047915 0.21049534616942142 chr17 81195210 2669172 0.03287351556822133 0.21659555898631958 chr18 78077248 2822398 0.036148789465530344 0.4651864109418595 chr19 59128983 1956893 0.03309532653385904 0.29742793243023374 chr20 63025520 2126924 0.033747028187946726 0.20816966901051268 chr21 48129895 1383750 0.02875032243473625 0.19161444710930178 chr22 51304566 1170021 0.02280539708687917 0.1634427335773018 chrMT 16571 22634 1.3658801520728985 1.45965111318087 chrX 155270560 5686091 0.03662053514845313 0.22808840485107562 chrY 59373566 249787 0.004207040554040497 0.09310296714845645