BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504606.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 = 422,801,300 number of mapped reads = 362,970,846 (85.85%) number of supplementary alignments = 1,971,515 (0.47%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 181,674,496 number of mapped paired reads (second in pair) = 181,296,350 number of mapped paired reads (both in pair) = 360,539,246 number of mapped paired reads (singletons) = 2,431,600 number of mapped bases = 36,029,844,422 bp number of sequenced bases = 36,020,374,975 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 88,700,878 duplication rate = 21.79% >>>>>>> Insert size mean insert size = 30,862.5416 std insert size = 1,716,264.4564 median insert size = 213 >>>>>>> Mapping quality mean mapping quality = 53.9598 >>>>>>> ACTG content number of A's = 9,492,694,526 bp (26.35%) number of C's = 8,414,805,208 bp (23.36%) number of T's = 9,512,206,004 bp (26.41%) number of G's = 8,567,966,391 bp (23.79%) number of N's = 32,702,846 bp (0.09%) GC percentage = 47.15% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 242,100,821 number of insertions = 2,720,616 mapped reads with insertion percentage = 0.73% number of deletions = 3,718,134 mapped reads with deletion percentage = 0.99% homopolymer indels = 40.27% >>>>>>> Coverage mean coverageData = 11.6387X std coverageData = 24.2079X There is a 78.3% of reference with a coverageData >= 1X There is a 69.59% of reference with a coverageData >= 2X There is a 62.25% of reference with a coverageData >= 3X There is a 56.15% of reference with a coverageData >= 4X There is a 50.89% of reference with a coverageData >= 5X There is a 46.36% of reference with a coverageData >= 6X There is a 42.39% of reference with a coverageData >= 7X There is a 38.9% of reference with a coverageData >= 8X There is a 35.81% of reference with a coverageData >= 9X There is a 33.06% of reference with a coverageData >= 10X There is a 30.61% of reference with a coverageData >= 11X There is a 28.41% of reference with a coverageData >= 12X There is a 26.42% of reference with a coverageData >= 13X There is a 24.62% of reference with a coverageData >= 14X There is a 22.99% of reference with a coverageData >= 15X There is a 21.51% of reference with a coverageData >= 16X There is a 20.16% of reference with a coverageData >= 17X There is a 18.92% of reference with a coverageData >= 18X There is a 17.78% of reference with a coverageData >= 19X There is a 16.74% of reference with a coverageData >= 20X There is a 15.78% of reference with a coverageData >= 21X There is a 14.89% of reference with a coverageData >= 22X There is a 14.07% of reference with a coverageData >= 23X There is a 13.31% of reference with a coverageData >= 24X There is a 12.6% of reference with a coverageData >= 25X There is a 11.95% of reference with a coverageData >= 26X There is a 11.34% of reference with a coverageData >= 27X There is a 10.77% of reference with a coverageData >= 28X There is a 10.24% of reference with a coverageData >= 29X There is a 9.74% of reference with a coverageData >= 30X There is a 9.28% of reference with a coverageData >= 31X There is a 8.85% of reference with a coverageData >= 32X There is a 8.44% of reference with a coverageData >= 33X There is a 8.06% of reference with a coverageData >= 34X There is a 7.7% of reference with a coverageData >= 35X There is a 7.36% of reference with a coverageData >= 36X There is a 7.04% of reference with a coverageData >= 37X There is a 6.74% of reference with a coverageData >= 38X There is a 6.46% of reference with a coverageData >= 39X There is a 6.19% of reference with a coverageData >= 40X There is a 5.94% of reference with a coverageData >= 41X There is a 5.7% of reference with a coverageData >= 42X There is a 5.48% of reference with a coverageData >= 43X There is a 5.26% of reference with a coverageData >= 44X There is a 5.06% of reference with a coverageData >= 45X There is a 4.87% of reference with a coverageData >= 46X There is a 4.68% of reference with a coverageData >= 47X There is a 4.51% of reference with a coverageData >= 48X There is a 4.35% of reference with a coverageData >= 49X There is a 4.19% of reference with a coverageData >= 50X There is a 4.04% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3702958602 14.856366604599152 25.159352015144215 chr2 243199373 2471288178 10.161572982344818 18.751632122590657 chr3 198022430 2667040256 13.468374547267196 22.386537589465092 chr4 191154276 1505404696 7.875338849338636 12.584408640412766 chr5 180915260 1464005615 8.092217400566431 13.66762287192679 chr6 171115067 1839926486 10.752568539157338 17.611390852284703 chr7 159138663 2929970727 18.411432343125817 27.518330115821616 chr8 146364022 2746426913 18.764358040119998 46.29446460791418 chr9 141213431 1416145747 10.028406908405193 19.60042891482199 chr10 135534747 1696922128 12.520199915966936 23.768435515943725 chr11 135006516 1837094975 13.607454139472795 23.13956223646723 chr12 133851895 1229076442 9.182361161192375 15.63467310906241 chr13 115169878 818160942 7.103949020420079 13.385157501372797 chr14 107349540 1203174761 11.208010402280252 19.596287005980088 chr15 102531392 803576446 7.837369905209129 14.679471109317697 chr16 90354753 1052110381 11.644217332983025 20.06847617565326 chr17 81195210 1309088486 16.12273046648934 49.83835804504739 chr18 78077248 470937178 6.031682597214492 28.065263923640444 chr19 59128983 1064523100 18.003406214512435 31.379038103645513 chr20 63025520 1622911635 25.75007132031596 38.54970378897801 chr21 48129895 341555548 7.0965363211367904 18.10546435087653 chr22 51304566 742147771 14.465530631328214 26.992164020548543 chrMT 16571 258613 15.606360509323517 12.68420006506773 chrX 155270560 1058838557 6.819313055868414 12.115644766089765 chrY 59373566 36300239 0.6113872122823143 14.555843158299894