BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618580.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 = 56,080,514 number of mapped reads = 53,875,786 (96.07%) number of supplementary alignments = 71,020 (0.13%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 27,265,883 number of mapped paired reads (second in pair) = 26,609,903 number of mapped paired reads (both in pair) = 52,736,400 number of mapped paired reads (singletons) = 1,139,386 number of mapped bases = 5,124,984,555 bp number of sequenced bases = 5,121,910,365 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,818,074 duplication rate = 20.87% >>>>>>> Insert size mean insert size = 27,845.3558 std insert size = 1,648,291.3506 median insert size = 203 >>>>>>> Mapping quality mean mapping quality = 52.3432 >>>>>>> ACTG content number of A's = 1,338,681,402 bp (26.14%) number of C's = 1,196,226,197 bp (23.36%) number of T's = 1,342,817,770 bp (26.22%) number of G's = 1,243,706,502 bp (24.28%) number of N's = 478,494 bp (0.01%) GC percentage = 47.64% >>>>>>> Mismatches and indels general error rate = 0.0135 number of mismatches = 67,673,833 number of insertions = 881,539 mapped reads with insertion percentage = 1.6% number of deletions = 2,161,078 mapped reads with deletion percentage = 3.92% homopolymer indels = 51.57% >>>>>>> Coverage mean coverageData = 1.6555X std coverageData = 8.0126X There is a 24.06% of reference with a coverageData >= 1X There is a 17.12% of reference with a coverageData >= 2X There is a 13.16% of reference with a coverageData >= 3X There is a 10.65% of reference with a coverageData >= 4X There is a 8.85% of reference with a coverageData >= 5X There is a 7.53% of reference with a coverageData >= 6X There is a 6.5% of reference with a coverageData >= 7X There is a 5.68% of reference with a coverageData >= 8X There is a 5.01% of reference with a coverageData >= 9X There is a 4.46% of reference with a coverageData >= 10X There is a 4% of reference with a coverageData >= 11X There is a 3.61% of reference with a coverageData >= 12X There is a 3.27% of reference with a coverageData >= 13X There is a 2.97% of reference with a coverageData >= 14X There is a 2.72% of reference with a coverageData >= 15X There is a 2.49% of reference with a coverageData >= 16X There is a 2.29% of reference with a coverageData >= 17X There is a 2.11% of reference with a coverageData >= 18X There is a 1.96% of reference with a coverageData >= 19X There is a 1.81% of reference with a coverageData >= 20X There is a 1.69% of reference with a coverageData >= 21X There is a 1.57% of reference with a coverageData >= 22X There is a 1.46% of reference with a coverageData >= 23X There is a 1.37% of reference with a coverageData >= 24X There is a 1.28% of reference with a coverageData >= 25X There is a 1.2% of reference with a coverageData >= 26X There is a 1.13% of reference with a coverageData >= 27X There is a 1.06% of reference with a coverageData >= 28X There is a 1% of reference with a coverageData >= 29X There is a 0.94% of reference with a coverageData >= 30X There is a 0.89% of reference with a coverageData >= 31X There is a 0.84% of reference with a coverageData >= 32X There is a 0.8% of reference with a coverageData >= 33X There is a 0.76% of reference with a coverageData >= 34X There is a 0.72% of reference with a coverageData >= 35X There is a 0.68% of reference with a coverageData >= 36X There is a 0.65% of reference with a coverageData >= 37X There is a 0.61% of reference with a coverageData >= 38X There is a 0.58% of reference with a coverageData >= 39X There is a 0.56% of reference with a coverageData >= 40X There is a 0.53% of reference with a coverageData >= 41X There is a 0.5% of reference with a coverageData >= 42X There is a 0.48% of reference with a coverageData >= 43X There is a 0.46% of reference with a coverageData >= 44X There is a 0.44% of reference with a coverageData >= 45X There is a 0.42% of reference with a coverageData >= 46X There is a 0.4% of reference with a coverageData >= 47X There is a 0.38% of reference with a coverageData >= 48X There is a 0.37% of reference with a coverageData >= 49X There is a 0.35% of reference with a coverageData >= 50X There is a 0.34% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 497814761 1.9972458203022891 8.113851621033326 chr2 243199373 421664309 1.733821530041527 9.632122230762418 chr3 198022430 303667126 1.5334986344728725 6.096475571393057 chr4 191154276 223975851 1.171702018321578 5.860755013570339 chr5 180915260 251688174 1.3911937224090438 5.758675682648196 chr6 171115067 264443813 1.5454151270033982 6.183213718850919 chr7 159138663 244470649 1.5362115301923833 6.002628948150553 chr8 146364022 246201902 1.6821203642518106 7.479624412147694 chr9 141213431 236927244 1.6777953932724714 8.022791368652454 chr10 135534747 268147962 1.978444405846716 7.470190601563435 chr11 135006516 290792892 2.1539174598061623 8.158294158271195 chr12 133851895 241274044 1.802544850037424 8.184663296913433 chr13 115169878 117281321 1.0183332919741392 4.652539408842142 chr14 107349540 156313166 1.4561139805536194 6.378958956459514 chr15 102531392 187141488 1.8252116190912535 7.353614187351848 chr16 90354753 222613333 2.463770035429127 19.45428553042205 chr17 81195210 223402250 2.7514215432166504 9.533533368542924 chr18 78077248 121675160 1.558394578661379 6.5669890899206225 chr19 59128983 169161003 2.860881321094259 10.346423713998359 chr20 63025520 178296493 2.8289571113415644 9.279481722441938 chr21 48129895 74405776 1.5459368028955809 10.997980926611442 chr22 51304566 134222260 2.616185467780782 10.222986180544826 chrMT 16571 4685 0.282722829038682 1.1226802775621154 chrX 155270560 7135342 0.04595424915064388 1.1959515601540067 chrY 59373566 42263551 0.7118243664192243 7.385483673059824