BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1153342.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 64,330,008 number of mapped reads = 63,536,734 (98.77%) number of supplementary alignments = 444,527 (0.69%) number of secondary alignments = 0 number of mapped bases = 6,321,917,042 bp number of sequenced bases = 6,321,046,911 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 26,431,654 duplication rate = 33.7% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.7991 >>>>>>> ACTG content number of A's = 1,650,949,584 bp (26.12%) number of C's = 1,506,702,612 bp (23.84%) number of T's = 1,650,704,879 bp (26.11%) number of G's = 1,512,401,018 bp (23.93%) number of N's = 288,818 bp (0%) GC percentage = 47.76% >>>>>>> Mismatches and indels general error rate = 0.0032 number of mismatches = 19,221,665 number of insertions = 545,009 mapped reads with insertion percentage = 0.85% number of deletions = 386,977 mapped reads with deletion percentage = 0.6% homopolymer indels = 47.79% >>>>>>> Coverage mean coverageData = 2.0422X std coverageData = 20.5606X There is a 12.81% of reference with a coverageData >= 1X There is a 7.09% of reference with a coverageData >= 2X There is a 5.56% of reference with a coverageData >= 3X There is a 4.93% of reference with a coverageData >= 4X There is a 4.51% of reference with a coverageData >= 5X There is a 4.2% of reference with a coverageData >= 6X There is a 3.94% of reference with a coverageData >= 7X There is a 3.73% of reference with a coverageData >= 8X There is a 3.54% of reference with a coverageData >= 9X There is a 3.37% of reference with a coverageData >= 10X There is a 3.21% of reference with a coverageData >= 11X There is a 3.08% of reference with a coverageData >= 12X There is a 2.95% of reference with a coverageData >= 13X There is a 2.83% of reference with a coverageData >= 14X There is a 2.72% of reference with a coverageData >= 15X There is a 2.62% of reference with a coverageData >= 16X There is a 2.52% of reference with a coverageData >= 17X There is a 2.43% of reference with a coverageData >= 18X There is a 2.35% of reference with a coverageData >= 19X There is a 2.27% of reference with a coverageData >= 20X There is a 2.2% of reference with a coverageData >= 21X There is a 2.12% of reference with a coverageData >= 22X There is a 2.06% of reference with a coverageData >= 23X There is a 1.99% of reference with a coverageData >= 24X There is a 1.93% of reference with a coverageData >= 25X There is a 1.87% of reference with a coverageData >= 26X There is a 1.82% of reference with a coverageData >= 27X There is a 1.77% of reference with a coverageData >= 28X There is a 1.72% of reference with a coverageData >= 29X There is a 1.67% of reference with a coverageData >= 30X There is a 1.62% of reference with a coverageData >= 31X There is a 1.58% of reference with a coverageData >= 32X There is a 1.53% of reference with a coverageData >= 33X There is a 1.49% of reference with a coverageData >= 34X There is a 1.45% of reference with a coverageData >= 35X There is a 1.42% of reference with a coverageData >= 36X There is a 1.38% of reference with a coverageData >= 37X There is a 1.35% of reference with a coverageData >= 38X There is a 1.31% of reference with a coverageData >= 39X There is a 1.28% of reference with a coverageData >= 40X There is a 1.25% of reference with a coverageData >= 41X There is a 1.22% of reference with a coverageData >= 42X There is a 1.19% of reference with a coverageData >= 43X There is a 1.16% of reference with a coverageData >= 44X There is a 1.14% of reference with a coverageData >= 45X There is a 1.11% of reference with a coverageData >= 46X There is a 1.09% of reference with a coverageData >= 47X There is a 1.06% of reference with a coverageData >= 48X There is a 1.04% of reference with a coverageData >= 49X There is a 1.01% of reference with a coverageData >= 50X There is a 0.99% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 671093983 2.6924465837138274 22.216667062296032 chr2 243199373 411661011 1.6926894420899679 14.413108153018324 chr3 198022430 299237045 1.5111270223277231 12.528467179677206 chr4 191154276 240863755 1.2600490035598262 13.406971063553124 chr5 180915260 390973340 2.1610854717285872 28.58406552771633 chr6 171115067 250379026 1.4632202201107165 12.97837980429273 chr7 159138663 333615852 2.096384660464315 22.36887457979323 chr8 146364022 365487618 2.49711379207658 45.145030884119734 chr9 141213431 217011285 1.5367609402536222 14.194213651777421 chr10 135534747 285673069 2.107747830893874 18.077339440321374 chr11 135006516 293553174 2.174363006301118 15.482167140190652 chr12 133851895 295992088 2.2113402877112796 17.15383910337097 chr13 115169878 94412221 0.8197648781046725 9.252853423698047 chr14 107349540 162174707 1.5107163663672896 12.825559491635905 chr15 102531392 314283710 3.065243764563345 24.498489577587755 chr16 90354753 259189308 2.8685741413072092 21.357713936689205 chr17 81195210 260792941 3.211925198543116 19.61650817115355 chr18 78077248 78937129 1.0110132083548846 9.351558063666316 chr19 59128983 378397382 6.399524612151709 34.664331110881236 chr20 63025520 138502617 2.1975640502450435 16.315044477942774 chr21 48129895 81498300 1.6932989361393787 24.427343881254327 chr22 51304566 107251139 2.0904794126900907 16.078858850633388 chrMT 16571 1514 0.09136443183875445 0.3278987741218513 chrX 155270560 383417170 2.4693487934866725 20.921238713172293 chrY 59373566 7517658 0.12661624535066665 5.989213318064316