BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008780.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 = 2,059,593 number of mapped reads = 1,857,816 (90.2%) number of supplementary alignments = 10,326 (0.5%) number of secondary alignments = 0 number of mapped bases = 123,794,615 bp number of sequenced bases = 123,731,558 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 85,982 duplication rate = 3.68% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1807 >>>>>>> ACTG content number of A's = 32,964,942 bp (26.64%) number of C's = 24,077,622 bp (19.46%) number of T's = 37,968,418 bp (30.69%) number of G's = 28,546,509 bp (23.07%) number of N's = 174,067 bp (0.14%) GC percentage = 42.53% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,013,665 number of insertions = 8,756 mapped reads with insertion percentage = 0.46% number of deletions = 35,521 mapped reads with deletion percentage = 1.89% homopolymer indels = 45.74% >>>>>>> Coverage mean coverageData = 0.04X std coverageData = 0.3524X There is a 3.17% of reference with a coverageData >= 1X There is a 0.59% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% 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 15039077 0.06033716963136473 0.5894057405474984 chr2 243199373 11581162 0.047620032309869484 0.47206802141541887 chr3 198022430 9704581 0.04900748364718078 0.29841765222691613 chr4 191154276 5102266 0.02669187478704374 0.2018398955991158 chr5 180915260 5362537 0.02964115354337716 0.20563168653742475 chr6 171115067 6683120 0.039056291869376994 0.2727801745162769 chr7 159138663 6009094 0.03776011364378498 0.3709353156084872 chr8 146364022 7236499 0.049441788365176244 0.381329275429493 chr9 141213431 3337119 0.023631739391701347 0.21903258611081847 chr10 135534747 7486657 0.05523791622232489 0.6404945944454911 chr11 135006516 5240258 0.03881485246238041 0.2826012297990767 chr12 133851895 6027947 0.045034453938810504 0.2564560931839514 chr13 115169878 3139849 0.027262762230242182 0.19968846436144413 chr14 107349540 3321819 0.030943951879067205 0.2151948627783419 chr15 102531392 2880715 0.02809593182934647 0.20151906962613536 chr16 90354753 3818060 0.04225632712426318 0.3284589603912913 chr17 81195210 4262580 0.05249792444652831 0.3184733507196267 chr18 78077248 1772606 0.02270323359757762 0.3191142821129161 chr19 59128983 3630147 0.06139369926250888 0.45376032161046176 chr20 63025520 2819827 0.044741035060083596 0.2619556948114001 chr21 48129895 1672173 0.03474291809695409 0.23394635695065344 chr22 51304566 1784396 0.03478045209465372 0.22624875007529344 chrMT 16571 87595 5.286041880393459 3.944062643118857 chrX 155270560 5506348 0.035462923557434196 0.23902055785113757 chrY 59373566 288183 0.004853725646190765 0.14307495536991344