BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124836.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 66,333,856 number of mapped reads = 62,965,476 (94.92%) number of supplementary alignments = 3,194,890 (4.82%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 31,759,533 number of mapped paired reads (second in pair) = 31,205,943 number of mapped paired reads (both in pair) = 61,919,574 number of mapped paired reads (singletons) = 1,045,902 number of mapped bases = 8,204,897,306 bp number of sequenced bases = 8,198,566,314 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 22,837,970 duplication rate = 23.29% >>>>>>> Insert size mean insert size = 330,887.2409 std insert size = 5,546,271.4194 median insert size = 237 >>>>>>> Mapping quality mean mapping quality = 52.8049 >>>>>>> ACTG content number of A's = 2,378,020,229 bp (29.01%) number of C's = 1,568,849,956 bp (19.14%) number of T's = 2,458,199,580 bp (29.98%) number of G's = 1,793,158,759 bp (21.87%) number of N's = 337,790 bp (0%) GC percentage = 41.01% >>>>>>> Mismatches and indels general error rate = 0.0148 number of mismatches = 116,804,966 number of insertions = 1,493,286 mapped reads with insertion percentage = 2.21% number of deletions = 3,110,710 mapped reads with deletion percentage = 4.73% homopolymer indels = 44.17% >>>>>>> Coverage mean coverageData = 2.6504X std coverageData = 35.6025X There is a 46.23% of reference with a coverageData >= 1X There is a 34.7% of reference with a coverageData >= 2X There is a 26.82% of reference with a coverageData >= 3X There is a 21.53% of reference with a coverageData >= 4X There is a 17.43% of reference with a coverageData >= 5X There is a 14.35% of reference with a coverageData >= 6X There is a 11.91% of reference with a coverageData >= 7X There is a 9.97% of reference with a coverageData >= 8X There is a 8.41% of reference with a coverageData >= 9X There is a 7.14% of reference with a coverageData >= 10X There is a 6.1% of reference with a coverageData >= 11X There is a 5.23% of reference with a coverageData >= 12X There is a 4.51% of reference with a coverageData >= 13X There is a 3.9% of reference with a coverageData >= 14X There is a 3.39% of reference with a coverageData >= 15X There is a 2.95% of reference with a coverageData >= 16X There is a 2.58% of reference with a coverageData >= 17X There is a 2.27% of reference with a coverageData >= 18X There is a 1.99% of reference with a coverageData >= 19X There is a 1.76% of reference with a coverageData >= 20X There is a 1.56% of reference with a coverageData >= 21X There is a 1.38% of reference with a coverageData >= 22X There is a 1.23% of reference with a coverageData >= 23X There is a 1.09% of reference with a coverageData >= 24X There is a 0.97% of reference with a coverageData >= 25X There is a 0.87% of reference with a coverageData >= 26X There is a 0.78% of reference with a coverageData >= 27X There is a 0.7% of reference with a coverageData >= 28X There is a 0.63% of reference with a coverageData >= 29X There is a 0.57% of reference with a coverageData >= 30X There is a 0.51% of reference with a coverageData >= 31X There is a 0.46% of reference with a coverageData >= 32X There is a 0.42% of reference with a coverageData >= 33X There is a 0.38% of reference with a coverageData >= 34X There is a 0.35% of reference with a coverageData >= 35X There is a 0.32% of reference with a coverageData >= 36X There is a 0.29% of reference with a coverageData >= 37X There is a 0.27% of reference with a coverageData >= 38X There is a 0.24% of reference with a coverageData >= 39X There is a 0.22% of reference with a coverageData >= 40X There is a 0.21% of reference with a coverageData >= 41X There is a 0.19% of reference with a coverageData >= 42X There is a 0.18% of reference with a coverageData >= 43X There is a 0.16% of reference with a coverageData >= 44X There is a 0.15% of reference with a coverageData >= 45X There is a 0.14% of reference with a coverageData >= 46X There is a 0.13% of reference with a coverageData >= 47X There is a 0.12% of reference with a coverageData >= 48X There is a 0.11% of reference with a coverageData >= 49X There is a 0.11% of reference with a coverageData >= 50X There is a 0.1% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 660866031 2.6514117732127938 36.9851614791738 chr2 243199373 774322340 3.183899409148559 38.847942537701236 chr3 198022430 549181093 2.773327713431251 6.487012348267567 chr4 191154276 570561697 2.9848230912710525 24.34956466928957 chr5 180915260 508193561 2.809014347380094 6.361636810050559 chr6 171115067 485081118 2.834824112829293 15.940353912721049 chr7 159138663 429079971 2.696264772565043 28.444645479641324 chr8 146364022 412652189 2.819355353599124 8.705350874971936 chr9 141213431 359592544 2.5464471860328923 48.751017473450524 chr10 135534747 473574130 3.4941160143974 116.73119605999834 chr11 135006516 382251555 2.831356339867329 25.921650122227565 chr12 133851895 358857224 2.6810021927593928 14.365542938800003 chr13 115169878 255674120 2.2199738719876043 4.829167635373902 chr14 107349540 237360495 2.211099320965884 6.21127812590447 chr15 102531392 225150370 2.195916446740526 7.843506967565819 chr16 90354753 273306101 3.024811555845878 46.63738109100469 chr17 81195210 200115360 2.464620265160962 35.606006357873035 chr18 78077248 227679222 2.916076422160781 43.58207549987185 chr19 59128983 108257382 1.8308683239148558 20.25818283564616 chr20 63025520 162503985 2.578383883226985 9.048545524056422 chr21 48129895 102949428 2.1389913275314645 12.100936131709448 chr22 51304566 78037961 1.5210724324224865 5.523511409784718 chrMT 16571 2998178 180.92921368656087 86.51391031958538 chrX 155270560 269648814 1.736638381416284 8.768161571818318 chrY 59373566 97002437 1.6337647127342831 39.08620739219645