BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818916.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 3,298,204 number of mapped reads = 3,232,620 (98.01%) number of supplementary alignments = 45,324 (1.37%) number of secondary alignments = 0 number of mapped bases = 299,375,843 bp number of sequenced bases = 299,190,452 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 992,735 duplication rate = 25.68% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.2762 >>>>>>> ACTG content number of A's = 84,894,843 bp (28.37%) number of C's = 65,958,265 bp (22.05%) number of T's = 85,714,451 bp (28.65%) number of G's = 62,618,741 bp (20.93%) number of N's = 4,152 bp (0%) GC percentage = 42.97% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 1,820,550 number of insertions = 40,830 mapped reads with insertion percentage = 1.22% number of deletions = 94,966 mapped reads with deletion percentage = 2.87% homopolymer indels = 42.13% >>>>>>> Coverage mean coverageData = 0.0967X std coverageData = 1.1692X There is a 5.69% of reference with a coverageData >= 1X There is a 2.02% of reference with a coverageData >= 2X There is a 0.84% of reference with a coverageData >= 3X There is a 0.38% of reference with a coverageData >= 4X There is a 0.19% of reference with a coverageData >= 5X There is a 0.1% of reference with a coverageData >= 6X There is a 0.06% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% 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 28522550 0.11443321539407518 1.9008625952142892 chr2 243199373 22629771 0.0930502851255295 1.5540576181349282 chr3 198022430 18333120 0.09258102731089604 0.4678469691441749 chr4 191154276 14859638 0.0777363620157783 0.6354798833897307 chr5 180915260 13158544 0.07273319011342659 0.4421745483422389 chr6 171115067 14699257 0.08590276272983022 0.5146311134990316 chr7 159138663 26807288 0.16845238922234756 2.678728642008868 chr8 146364022 25908661 0.17701522987664278 0.9170295532826698 chr9 141213431 11019960 0.078037619523599 0.9734044883652625 chr10 135534747 14003337 0.10331916582247355 1.5848124359444595 chr11 135006516 13255600 0.09818489057224468 0.6692580196596815 chr12 133851895 11556443 0.08633753747005225 0.45541069692483305 chr13 115169878 9054484 0.07861850821792135 0.42545115224551333 chr14 107349540 8809991 0.08206826969170058 0.4981628065989982 chr15 102531392 8334060 0.0812830084273117 0.4374274494041285 chr16 90354753 7654842 0.08471985972890657 1.0813597966120183 chr17 81195210 7538892 0.09284897471168557 0.688292228156625 chr18 78077248 5784716 0.07408965029095288 1.1883865973373031 chr19 59128983 5417364 0.09161943475334254 1.7010909568082155 chr20 63025520 12609545 0.20007046352017405 0.779136047891932 chr21 48129895 2923581 0.060743556577466044 0.5181476950605771 chr22 51304566 2813789 0.054844806600644475 0.41301153881791197 chrMT 16571 350983 21.18055639369984 13.7552184339137 chrX 155270560 12220329 0.07870345157510863 0.5760325014821435 chrY 59373566 1109098 0.01867999641456604 1.282019613781396