BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1777260.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP052908/SRP052908.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 = 16,087,630 number of mapped reads = 15,822,941 (98.35%) number of supplementary alignments = 584,804 (3.64%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,926,988 number of mapped paired reads (second in pair) = 7,895,953 number of mapped paired reads (both in pair) = 15,746,360 number of mapped paired reads (singletons) = 76,581 number of mapped bases = 1,560,249,366 bp number of sequenced bases = 1,559,884,625 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 852,482 duplication rate = 4.35% >>>>>>> Insert size mean insert size = 172,815.2372 std insert size = 4,043,668.7672 median insert size = 178 >>>>>>> Mapping quality mean mapping quality = 53.273 >>>>>>> ACTG content number of A's = 463,928,447 bp (29.74%) number of C's = 317,052,503 bp (20.33%) number of T's = 454,355,645 bp (29.13%) number of G's = 324,536,565 bp (20.81%) number of N's = 11,465 bp (0%) GC percentage = 41.13% >>>>>>> Mismatches and indels general error rate = 0.0045 number of mismatches = 6,415,362 number of insertions = 394,542 mapped reads with insertion percentage = 2.45% number of deletions = 163,872 mapped reads with deletion percentage = 1.02% homopolymer indels = 50.42% >>>>>>> Coverage mean coverageData = 0.504X std coverageData = 2.3483X There is a 27.9% of reference with a coverageData >= 1X There is a 12.64% of reference with a coverageData >= 2X There is a 5.11% of reference with a coverageData >= 3X There is a 2.19% of reference with a coverageData >= 4X There is a 0.93% of reference with a coverageData >= 5X There is a 0.41% of reference with a coverageData >= 6X There is a 0.19% of reference with a coverageData >= 7X There is a 0.09% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% 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 132491576 0.5315596625935789 4.842058948684651 chr2 243199373 148708915 0.6114691545689142 1.7599427143989372 chr3 198022430 104195058 0.5261780597278803 1.0505917922629726 chr4 191154276 96064447 0.5025492968831102 1.061874661275562 chr5 180915260 105172736 0.5813370082766927 1.0767535523411766 chr6 171115067 74625093 0.4361105910094989 1.417440224061908 chr7 159138663 105391851 0.6622642732646309 2.023664335901335 chr8 146364022 77034926 0.5263241946166252 1.2619683135744006 chr9 141213431 55466709 0.3927863561363366 2.4080208947389963 chr10 135534747 71589697 0.5282017975803651 3.4410870683767487 chr11 135006516 90876330 0.6731255104753611 1.568067096841979 chr12 133851895 72824225 0.5440657003772714 1.047675671269375 chr13 115169878 67748644 0.5882496810494147 1.0983919500343111 chr14 107349540 31876402 0.2969402756639665 0.7744346644655803 chr15 102531392 57439582 0.5602145926195949 1.139695960292022 chr16 90354753 40933778 0.4530340313143239 1.9334187009992378 chr17 81195210 38199414 0.47046388573907255 1.3779350060395887 chr18 78077248 33804454 0.4329616484433468 2.7888992713300254 chr19 59128983 28874684 0.4883338514379657 2.871582763276609 chr20 63025520 39593905 0.6282202034985194 1.1476816454889762 chr21 48129895 14470823 0.3006618443692844 0.9480026548913347 chr22 51304566 11543317 0.22499589997506264 0.683248856395986 chrMT 16571 7347898 443.41910566652587 90.63886523938581 chrX 155270560 51895525 0.3342264303033363 0.9548107217449815 chrY 59373566 2079377 0.035021932150748704 0.929497731108475