BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618651.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 78,430,591 number of mapped reads = 62,293,553 (79.43%) number of supplementary alignments = 382,520 (0.49%) number of secondary alignments = 0 number of mapped bases = 5,946,109,513 bp number of sequenced bases = 5,940,454,243 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 42,025,207 duplication rate = 52.58% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.4532 >>>>>>> ACTG content number of A's = 1,590,007,485 bp (26.77%) number of C's = 1,342,698,008 bp (22.6%) number of T's = 1,888,045,941 bp (31.78%) number of G's = 1,119,328,358 bp (18.84%) number of N's = 374,451 bp (0.01%) GC percentage = 41.45% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 53,762,646 number of insertions = 1,479,187 mapped reads with insertion percentage = 2.28% number of deletions = 3,130,528 mapped reads with deletion percentage = 4.85% homopolymer indels = 46.13% >>>>>>> Coverage mean coverageData = 1.9208X std coverageData = 54.6225X There is a 16.98% of reference with a coverageData >= 1X There is a 11.12% of reference with a coverageData >= 2X There is a 8.14% of reference with a coverageData >= 3X There is a 6.28% of reference with a coverageData >= 4X There is a 5.04% of reference with a coverageData >= 5X There is a 4.19% of reference with a coverageData >= 6X There is a 3.57% of reference with a coverageData >= 7X There is a 3.11% of reference with a coverageData >= 8X There is a 2.75% of reference with a coverageData >= 9X There is a 2.47% of reference with a coverageData >= 10X There is a 2.24% of reference with a coverageData >= 11X There is a 2.05% of reference with a coverageData >= 12X There is a 1.89% of reference with a coverageData >= 13X There is a 1.76% of reference with a coverageData >= 14X There is a 1.64% of reference with a coverageData >= 15X There is a 1.54% of reference with a coverageData >= 16X There is a 1.45% of reference with a coverageData >= 17X There is a 1.37% of reference with a coverageData >= 18X There is a 1.3% of reference with a coverageData >= 19X There is a 1.24% of reference with a coverageData >= 20X There is a 1.18% of reference with a coverageData >= 21X There is a 1.13% of reference with a coverageData >= 22X There is a 1.08% of reference with a coverageData >= 23X There is a 1.04% of reference with a coverageData >= 24X There is a 1% of reference with a coverageData >= 25X There is a 0.96% of reference with a coverageData >= 26X There is a 0.93% of reference with a coverageData >= 27X There is a 0.9% of reference with a coverageData >= 28X There is a 0.87% of reference with a coverageData >= 29X There is a 0.84% of reference with a coverageData >= 30X There is a 0.81% of reference with a coverageData >= 31X There is a 0.79% of reference with a coverageData >= 32X There is a 0.77% of reference with a coverageData >= 33X There is a 0.75% of reference with a coverageData >= 34X There is a 0.72% of reference with a coverageData >= 35X There is a 0.71% of reference with a coverageData >= 36X There is a 0.69% of reference with a coverageData >= 37X There is a 0.67% of reference with a coverageData >= 38X There is a 0.65% of reference with a coverageData >= 39X There is a 0.64% of reference with a coverageData >= 40X There is a 0.62% of reference with a coverageData >= 41X There is a 0.61% of reference with a coverageData >= 42X There is a 0.6% of reference with a coverageData >= 43X There is a 0.58% of reference with a coverageData >= 44X There is a 0.57% of reference with a coverageData >= 45X There is a 0.56% of reference with a coverageData >= 46X There is a 0.55% of reference with a coverageData >= 47X There is a 0.54% of reference with a coverageData >= 48X There is a 0.53% of reference with a coverageData >= 49X There is a 0.52% of reference with a coverageData >= 50X There is a 0.51% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 513122457 2.058660696375958 49.25486236591207 chr2 243199373 554079053 2.2782914534898904 123.67689143750671 chr3 198022430 421057222 2.126310751766858 48.90593682374353 chr4 191154276 313504160 1.6400583160378792 38.947521452307704 chr5 180915260 348489486 1.9262581055904295 37.14137791968182 chr6 171115067 336108536 1.9642252543430323 32.876065831183595 chr7 159138663 282685005 1.7763439736828754 33.21943788008664 chr8 146364022 296342539 2.024695242386821 36.976909315409166 chr9 141213431 240551067 1.703457421128731 35.10723766733449 chr10 135534747 286157213 2.111319933330454 40.221431937212174 chr11 135006516 286309825 2.1207111588599177 37.7932467638131 chr12 133851895 278656169 2.0818246092070645 39.500792193039395 chr13 115169878 194642715 1.6900488077273121 36.987491918663 chr14 107349540 196190712 1.8275878219878725 33.36448530744792 chr15 102531392 174638170 1.7032653765200028 33.53048026801754 chr16 90354753 212151145 2.3479799120252145 124.61846928928196 chr17 81195210 146684084 1.806560805742112 31.65494129560888 chr18 78077248 138219965 1.7702976032147035 32.3500461477219 chr19 59128983 90554540 1.5314746746109265 27.10531768567802 chr20 63025520 147347211 2.3378975849782755 36.10272621620111 chr21 48129895 67309130 1.3984890264148717 34.296482490934 chr22 51304566 77532544 1.5112211260104997 41.97255703490835 chrMT 16571 39289 2.370949248687466 7.630674063332209 chrX 155270560 322361992 2.0761308003268617 35.38407659638798 chrY 59373566 21375284 0.36001347805183204 44.388593551613695