BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926987.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 29,221,276 number of mapped reads = 28,728,370 (98.31%) number of supplementary alignments = 540,242 (1.85%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 14,418,642 number of mapped paired reads (second in pair) = 14,309,728 number of mapped paired reads (both in pair) = 28,456,276 number of mapped paired reads (singletons) = 272,094 number of mapped bases = 2,748,798,392 bp number of sequenced bases = 2,746,731,787 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,025,974 duplication rate = 5.35% >>>>>>> Insert size mean insert size = 183,881.9085 std insert size = 4,240,594.8219 median insert size = 180 >>>>>>> Mapping quality mean mapping quality = 53.1592 >>>>>>> ACTG content number of A's = 772,456,806 bp (28.12%) number of C's = 572,529,988 bp (20.84%) number of T's = 779,482,384 bp (28.38%) number of G's = 622,016,779 bp (22.65%) number of N's = 245,830 bp (0.01%) GC percentage = 43.49% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 26,200,645 number of insertions = 444,811 mapped reads with insertion percentage = 1.52% number of deletions = 1,442,538 mapped reads with deletion percentage = 4.89% homopolymer indels = 52.67% >>>>>>> Coverage mean coverageData = 0.8879X std coverageData = 3.9057X There is a 31.83% of reference with a coverageData >= 1X There is a 18.79% of reference with a coverageData >= 2X There is a 11.44% of reference with a coverageData >= 3X There is a 7.42% of reference with a coverageData >= 4X There is a 4.97% of reference with a coverageData >= 5X There is a 3.41% of reference with a coverageData >= 6X There is a 2.4% of reference with a coverageData >= 7X There is a 1.71% of reference with a coverageData >= 8X There is a 1.24% of reference with a coverageData >= 9X There is a 0.91% of reference with a coverageData >= 10X There is a 0.68% of reference with a coverageData >= 11X There is a 0.51% of reference with a coverageData >= 12X There is a 0.39% of reference with a coverageData >= 13X There is a 0.3% of reference with a coverageData >= 14X There is a 0.23% of reference with a coverageData >= 15X There is a 0.18% of reference with a coverageData >= 16X There is a 0.14% of reference with a coverageData >= 17X There is a 0.12% of reference with a coverageData >= 18X There is a 0.09% of reference with a coverageData >= 19X There is a 0.08% of reference with a coverageData >= 20X There is a 0.06% of reference with a coverageData >= 21X There is a 0.05% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 252812184 1.0142890837571874 4.761137662513885 chr2 243199373 237380218 0.9760724917658402 6.519081359037944 chr3 198022430 144386446 0.7291418754935994 1.7733262074742489 chr4 191154276 168354033 0.8807233430655771 2.830022366012655 chr5 180915260 174386745 0.9639139617078184 1.9907551275988518 chr6 171115067 163433087 0.9551063495770363 3.6811931655926338 chr7 159138663 153547680 0.9648672240007445 3.1859833532258692 chr8 146364022 114428468 0.7818073488032462 2.247909271400706 chr9 141213431 124961346 0.884911195168114 5.528871401436487 chr10 135534747 144127135 1.0633962005329896 5.64038986944942 chr11 135006516 143523479 1.0630855698846418 3.5564569122891547 chr12 133851895 81177255 0.6064707189987859 1.9380526910632065 chr13 115169878 87700617 0.761489189039516 1.8172657990296535 chr14 107349540 70390392 0.6557120971361405 1.7866015987102994 chr15 102531392 86786683 0.8464401127022639 2.017046755989064 chr16 90354753 92855458 1.027676518577833 4.256321243451879 chr17 81195210 86615276 1.0667535190807438 4.095519007976049 chr18 78077248 77369112 0.9909303155766965 6.216921096782815 chr19 59128983 51352554 0.8684836334830924 3.1938053440953134 chr20 63025520 73094408 1.159758904012216 2.4860806743056107 chr21 48129895 37893172 0.7873105062872047 3.279794605078762 chr22 51304566 40502817 0.7894583300831353 2.1145778810636857 chrMT 16571 5506248 332.28217971154425 229.36119592398978 chrX 155270560 131581222 0.8474318763325127 2.2916648773871624 chrY 59373566 4632357 0.07802052852948062 2.465199179600431