BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926962.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 = 32,315,202 number of mapped reads = 31,319,332 (96.92%) number of supplementary alignments = 1,189,324 (3.68%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,628,701 number of mapped paired reads (second in pair) = 15,690,631 number of mapped paired reads (both in pair) = 30,722,492 number of mapped paired reads (singletons) = 596,840 number of mapped bases = 2,771,446,623 bp number of sequenced bases = 2,769,232,957 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,165,842 duplication rate = 10.6% >>>>>>> Insert size mean insert size = 359,183.585 std insert size = 5,856,512.508 median insert size = 167 >>>>>>> Mapping quality mean mapping quality = 52.3427 >>>>>>> ACTG content number of A's = 784,471,968 bp (28.33%) number of C's = 534,056,622 bp (19.29%) number of T's = 816,169,776 bp (29.47%) number of G's = 634,228,492 bp (22.9%) number of N's = 306,099 bp (0.01%) GC percentage = 42.19% >>>>>>> Mismatches and indels general error rate = 0.0106 number of mismatches = 28,636,325 number of insertions = 485,393 mapped reads with insertion percentage = 1.52% number of deletions = 1,485,212 mapped reads with deletion percentage = 4.62% homopolymer indels = 51.55% >>>>>>> Coverage mean coverageData = 0.8953X std coverageData = 3.4441X There is a 34.86% of reference with a coverageData >= 1X There is a 19.57% of reference with a coverageData >= 2X There is a 11.23% of reference with a coverageData >= 3X There is a 6.99% of reference with a coverageData >= 4X There is a 4.49% of reference with a coverageData >= 5X There is a 3.01% of reference with a coverageData >= 6X There is a 2.07% of reference with a coverageData >= 7X There is a 1.46% of reference with a coverageData >= 8X There is a 1.05% of reference with a coverageData >= 9X There is a 0.77% of reference with a coverageData >= 10X There is a 0.58% of reference with a coverageData >= 11X There is a 0.44% of reference with a coverageData >= 12X There is a 0.34% of reference with a coverageData >= 13X There is a 0.26% of reference with a coverageData >= 14X There is a 0.21% of reference with a coverageData >= 15X There is a 0.16% of reference with a coverageData >= 16X There is a 0.13% of reference with a coverageData >= 17X There is a 0.11% of reference with a coverageData >= 18X There is a 0.09% of reference with a coverageData >= 19X There is a 0.07% 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 0.04% 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 228609110 0.9171857188672762 3.32376855714585 chr2 243199373 244317587 1.0045979312619362 6.341032980971127 chr3 198022430 195797765 0.9887655908474611 2.0000213916066416 chr4 191154276 175615866 0.9187127260496124 2.91282521380301 chr5 180915260 170233665 0.9409580208988452 1.9052720349307999 chr6 171115067 155424158 0.908302002418057 2.521839800763233 chr7 159138663 144045296 0.905155876545224 2.6140393149346797 chr8 146364022 134937971 0.9219340187303681 2.1834248409380863 chr9 141213431 117644062 0.8330939993944344 3.907741625399667 chr10 135534747 134615001 0.9932139468264917 5.391738202732136 chr11 135006516 130724278 0.9682812494768771 4.175590455044719 chr12 133851895 123368958 0.9216825656446627 2.000188757790768 chr13 115169878 83129793 0.7218015200120296 1.6826345190578846 chr14 107349540 85129839 0.7930154055620545 1.8771239556144534 chr15 102531392 81228932 0.7922347528452555 1.8589332420775373 chr16 90354753 85764801 0.9492007686634925 6.750206432697885 chr17 81195210 69551201 0.8565924147495892 2.200935747277291 chr18 78077248 75107157 0.9619595839238596 3.9102203705599057 chr19 59128983 42159805 0.713014208277521 2.399039106698544 chr20 63025520 63897097 1.0138289537317582 2.198015875665366 chr21 48129895 32262299 0.6703172529256505 2.7647629787787524 chr22 51304566 32599801 0.6354171478616543 1.7418064165575962 chrMT 16571 440638 26.59091183392674 24.428550426358086 chrX 155270560 159866660 1.0296005888044715 2.3454384900583007 chrY 59373566 4974883 0.08378952680726638 2.5533177113289063