BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617654.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 30,342,101 (94.82%) number of supplementary alignments = 181,446 (0.57%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,340,241 number of mapped paired reads (second in pair) = 15,001,860 number of mapped paired reads (both in pair) = 29,643,538 number of mapped paired reads (singletons) = 698,563 number of mapped bases = 2,931,343,447 bp number of sequenced bases = 2,929,545,128 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,021,379 duplication rate = 10.81% >>>>>>> Insert size mean insert size = 47,490.5804 std insert size = 2,040,155.3643 median insert size = 224 >>>>>>> Mapping quality mean mapping quality = 52.5425 >>>>>>> ACTG content number of A's = 871,593,709 bp (29.75%) number of C's = 582,809,179 bp (19.89%) number of T's = 870,889,122 bp (29.73%) number of G's = 599,589,319 bp (20.47%) number of N's = 4,663,799 bp (0.16%) GC percentage = 40.36% >>>>>>> Mismatches and indels general error rate = 0.0146 number of mismatches = 41,876,330 number of insertions = 461,402 mapped reads with insertion percentage = 1.49% number of deletions = 1,080,245 mapped reads with deletion percentage = 3.48% homopolymer indels = 47.54% >>>>>>> Coverage mean coverageData = 0.9469X std coverageData = 10.528X There is a 33.29% of reference with a coverageData >= 1X There is a 19.26% of reference with a coverageData >= 2X There is a 11.76% of reference with a coverageData >= 3X There is a 7.51% of reference with a coverageData >= 4X There is a 4.94% of reference with a coverageData >= 5X There is a 3.34% of reference with a coverageData >= 6X There is a 2.32% of reference with a coverageData >= 7X There is a 1.64% of reference with a coverageData >= 8X There is a 1.19% of reference with a coverageData >= 9X There is a 0.88% of reference with a coverageData >= 10X There is a 0.66% 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 0.31% of reference with a coverageData >= 14X There is a 0.25% of reference with a coverageData >= 15X There is a 0.2% of reference with a coverageData >= 16X There is a 0.17% of reference with a coverageData >= 17X There is a 0.14% of reference with a coverageData >= 18X There is a 0.12% of reference with a coverageData >= 19X There is a 0.1% of reference with a coverageData >= 20X There is a 0.09% of reference with a coverageData >= 21X There is a 0.08% of reference with a coverageData >= 22X There is a 0.07% of reference with a coverageData >= 23X There is a 0.06% of reference with a coverageData >= 24X There is a 0.05% of reference with a coverageData >= 25X There is a 0.05% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.04% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.03% of reference with a coverageData >= 33X There is a 0.03% of reference with a coverageData >= 34X There is a 0.03% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 179731788 0.7210886266959391 10.217066469008548 chr2 243199373 302897584 1.2454702504516737 12.063573651614568 chr3 198022430 245661489 1.2405740551714268 2.49743745555149 chr4 191154276 163801931 0.8569095833357137 8.321226523011996 chr5 180915260 193916920 1.0718660216943556 2.344143931996786 chr6 171115067 142145343 0.8307003321922551 5.7737092727626 chr7 159138663 228838284 1.4379804359673425 13.186491620694166 chr8 146364022 130159194 0.8892840755633239 4.082087226442298 chr9 141213431 120229039 0.851399460721268 20.16052240434308 chr10 135534747 124320807 0.9172615122821604 21.371801269084465 chr11 135006516 161237583 1.1942948220365897 12.071515757900563 chr12 133851895 124956502 0.9335430178257842 2.226472503092246 chr13 115169878 125883792 1.0930270500069472 2.345294471064622 chr14 107349540 83980594 0.7823097704936602 2.496426475627114 chr15 102531392 62768806 0.6121911033842201 1.7700940791071456 chr16 90354753 81153331 0.8981633871546304 16.571277425041234 chr17 81195210 72561938 0.8936726439897131 12.634761436819963 chr18 78077248 54233761 0.6946167083143094 18.296560592355593 chr19 59128983 31159651 0.5269776244925437 6.077881186081741 chr20 63025520 79123813 1.2554249929235015 3.0868604057500044 chr21 48129895 42857736 0.8904597859604721 4.381766744410305 chr22 51304566 18992900 0.3701990189333246 1.2803945733753639 chrMT 16571 3104360 187.33691388570395 132.51814135124818 chrX 155270560 145886793 0.9395650598542312 4.414870022468048 chrY 59373566 11739508 0.19772280479161383 17.106263572406405