BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004004.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,508,092 number of mapped reads = 1,175,261 (77.93%) number of supplementary alignments = 10,116 (0.67%) number of secondary alignments = 0 number of mapped bases = 75,834,313 bp number of sequenced bases = 75,792,964 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 97,210 duplication rate = 6.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8439 >>>>>>> ACTG content number of A's = 20,064,414 bp (26.47%) number of C's = 14,604,200 bp (19.27%) number of T's = 23,335,913 bp (30.79%) number of G's = 17,773,698 bp (23.45%) number of N's = 14,739 bp (0.02%) GC percentage = 42.72% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 717,028 number of insertions = 5,820 mapped reads with insertion percentage = 0.49% number of deletions = 25,100 mapped reads with deletion percentage = 2.11% homopolymer indels = 47.22% >>>>>>> Coverage mean coverageData = 0.0245X std coverageData = 0.2606X There is a 1.66% of reference with a coverageData >= 1X There is a 0.5% of reference with a coverageData >= 2X There is a 0.17% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% 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 6776892 0.027189067665351976 0.3460436731361552 chr2 243199373 6319507 0.025984881959379064 0.3372885110315313 chr3 198022430 4876004 0.02462349340930722 0.21838085871143487 chr4 191154276 4892636 0.025595221317466107 0.22412384454081638 chr5 180915260 4510689 0.02493260656950663 0.21854379521235057 chr6 171115067 4689555 0.027405856668366906 0.24817285573520845 chr7 159138663 4178099 0.02625445583893086 0.3276254226733287 chr8 146364022 4409131 0.030124418144234926 0.28184890679023844 chr9 141213431 2911810 0.020619922477487288 0.23335649364819655 chr10 135534747 3529607 0.0260420820352437 0.2433082549663968 chr11 135006516 3550743 0.026300530561058254 0.26818015668099854 chr12 133851895 3216711 0.024031867460673605 0.2147364311967231 chr13 115169878 2112048 0.01833854508381089 0.18757602279366742 chr14 107349540 2053414 0.01912829808120277 0.20459397729916903 chr15 102531392 2116401 0.020641492900047628 0.20124687185803275 chr16 90354753 2186722 0.024201515995511604 0.22490372006601708 chr17 81195210 2021428 0.024895902110481642 0.2319157417445338 chr18 78077248 2072790 0.026547938779809453 0.37137505326612597 chr19 59128983 1474306 0.02493372835450256 0.2887915994048192 chr20 63025520 1880206 0.02983245517054044 0.24760798782252266 chr21 48129895 1055046 0.021920804107301708 0.2124038582221514 chr22 51304566 876119 0.017076823142797855 0.18342112913278202 chrMT 16571 81478 4.9169030233540525 4.519732523159572 chrX 155270560 3852290 0.024810176507381695 0.22510933569440525 chrY 59373566 190681 0.0032115470376160326 0.07867005829932948