BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818880.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 = 1,715,584 number of mapped reads = 1,688,411 (98.42%) number of supplementary alignments = 22,570 (1.32%) number of secondary alignments = 0 number of mapped bases = 156,509,711 bp number of sequenced bases = 156,413,008 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 286,399 duplication rate = 13.82% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.3359 >>>>>>> ACTG content number of A's = 43,448,720 bp (27.78%) number of C's = 32,747,328 bp (20.94%) number of T's = 44,819,643 bp (28.65%) number of G's = 35,395,022 bp (22.63%) number of N's = 2,295 bp (0%) GC percentage = 43.57% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 930,037 number of insertions = 19,069 mapped reads with insertion percentage = 1.09% number of deletions = 48,420 mapped reads with deletion percentage = 2.8% homopolymer indels = 42.36% >>>>>>> Coverage mean coverageData = 0.0506X std coverageData = 0.6433X There is a 3.75% of reference with a coverageData >= 1X There is a 0.8% of reference with a coverageData >= 2X There is a 0.22% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% 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% 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 14687360 0.05892607184316704 1.0104375611034209 chr2 243199373 11672294 0.047994753670684835 0.7855656146340088 chr3 198022430 9447183 0.04770764099804249 0.2772993936578787 chr4 191154276 7674827 0.04014991011762666 0.35856366648358384 chr5 180915260 6810153 0.03764277817139361 0.2590149856597152 chr6 171115067 7558879 0.04417424562619024 0.29715807388695986 chr7 159138663 13794950 0.08668509424387963 1.526212263996475 chr8 146364022 13319721 0.0910040651930158 0.5107672571408757 chr9 141213431 5757706 0.04077307632303049 0.5598886174846843 chr10 135534747 7353213 0.05425334213373342 0.9135273731634478 chr11 135006516 6775723 0.0501881183275628 0.3724492554581256 chr12 133851895 5964880 0.04456328391914063 0.269533201506068 chr13 115169878 4684771 0.040677050990711304 0.2515053305985348 chr14 107349540 4553142 0.04241417336301581 0.28630178597040407 chr15 102531392 4263622 0.04158357666693924 0.26271137750812984 chr16 90354753 3870540 0.04283714881053352 0.5334137562307364 chr17 81195210 3939106 0.04851401948464694 0.4123505146931801 chr18 78077248 3000092 0.038424663738148145 0.6338054181182282 chr19 59128983 2780511 0.047024502349380846 0.8859457077319337 chr20 63025520 6486471 0.10291816711706624 0.4456043063642906 chr21 48129895 1502641 0.031220533516642827 0.28039378205604376 chr22 51304566 1455240 0.028364726835424355 0.23503369217273418 chrMT 16571 277492 16.745639973447588 10.448661797614472 chrX 155270560 8258519 0.05318792564411438 0.3671743687168119 chrY 59373566 620675 0.010453726158203131 0.6742477165833491