BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818838.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 = 1,843,625 number of mapped reads = 1,819,344 (98.68%) number of supplementary alignments = 31,063 (1.68%) number of secondary alignments = 0 number of mapped bases = 168,279,932 bp number of sequenced bases = 168,170,480 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 526,655 duplication rate = 25.06% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.5722 >>>>>>> ACTG content number of A's = 48,279,255 bp (28.71%) number of C's = 36,226,223 bp (21.54%) number of T's = 47,452,784 bp (28.22%) number of G's = 36,209,869 bp (21.53%) number of N's = 2,349 bp (0%) GC percentage = 43.07% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 1,005,400 number of insertions = 20,928 mapped reads with insertion percentage = 1.11% number of deletions = 55,631 mapped reads with deletion percentage = 2.99% homopolymer indels = 41.71% >>>>>>> Coverage mean coverageData = 0.0544X std coverageData = 0.6207X There is a 3.4% of reference with a coverageData >= 1X There is a 1.14% of reference with a coverageData >= 2X There is a 0.43% of reference with a coverageData >= 3X There is a 0.18% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% 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 16085037 0.06453358846395812 0.8764138365826192 chr2 243199373 12688378 0.0521727414157437 0.9639925153561071 chr3 198022430 10660525 0.05383493677963653 0.3377756195548281 chr4 191154276 8401206 0.04394987219642421 0.4016795066232607 chr5 180915260 7500474 0.0414584927772262 0.31549160236383056 chr6 171115067 8247468 0.0481983740216167 0.35161402659850094 chr7 159138663 14918667 0.09374633868829224 1.2417730801219768 chr8 146364022 14802006 0.10113145155303262 0.5584674480328099 chr9 141213431 6279006 0.044464651524542306 0.5351728507646887 chr10 135534747 7383985 0.054480383543269534 0.7797706134473994 chr11 135006516 7449575 0.05517937371259918 0.4068171521632563 chr12 133851895 6647374 0.049662158313111666 0.32680544651871196 chr13 115169878 5243884 0.04553173183008842 0.31251885013635017 chr14 107349540 5025966 0.04681870085330594 0.338676656366367 chr15 102531392 4683347 0.045677200988356814 0.31267114216855596 chr16 90354753 4223589 0.04674451381655595 0.6896019222011482 chr17 81195210 4125035 0.05080392057610295 0.39528310796402255 chr18 78077248 3252376 0.04165587393654038 0.5565264152740399 chr19 59128983 2895157 0.048963416130461776 0.7027694596223393 chr20 63025520 6996923 0.11101729902426827 0.5245396004207454 chr21 48129895 1668016 0.03465654766128204 0.3264267660112048 chr22 51304566 1578556 0.03076833356313744 0.29957531664543247 chrMT 16571 78053 4.710216643533885 4.114048745760569 chrX 155270560 6826622 0.04396597783894127 0.35076183706600456 chrY 59373566 618707 0.010420580094515462 0.8370344866470567