BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818742.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 = 2,341,421 number of mapped reads = 2,272,055 (97.04%) number of supplementary alignments = 17,838 (0.76%) number of secondary alignments = 0 number of mapped bases = 154,365,971 bp number of sequenced bases = 154,302,337 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,109,548 duplication rate = 40.97% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.6881 >>>>>>> ACTG content number of A's = 45,698,531 bp (29.62%) number of C's = 31,529,675 bp (20.43%) number of T's = 44,284,068 bp (28.7%) number of G's = 32,780,451 bp (21.24%) number of N's = 9,612 bp (0.01%) GC percentage = 41.68% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 769,109 number of insertions = 23,479 mapped reads with insertion percentage = 1.02% number of deletions = 39,619 mapped reads with deletion percentage = 1.73% homopolymer indels = 37.89% >>>>>>> Coverage mean coverageData = 0.0499X std coverageData = 0.5838X There is a 2.14% of reference with a coverageData >= 1X There is a 1.09% of reference with a coverageData >= 2X There is a 0.64% of reference with a coverageData >= 3X There is a 0.39% of reference with a coverageData >= 4X There is a 0.24% of reference with a coverageData >= 5X There is a 0.15% of reference with a coverageData >= 6X There is a 0.09% of reference with a coverageData >= 7X There is a 0.06% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% 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% 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 12568459 0.050424985701439835 0.8553772157568822 chr2 243199373 13615551 0.05598514022484754 0.8651805921062554 chr3 198022430 10493821 0.05299309275216954 0.4582554560079393 chr4 191154276 10214265 0.05343466656220654 0.4994279010890536 chr5 180915260 9705795 0.0536482936818044 0.4665684213781072 chr6 171115067 9222826 0.05389838639983702 0.5024365057381601 chr7 159138663 8468277 0.05321319684582244 0.5237748170963955 chr8 146364022 8084609 0.05523631347053308 0.5353020389766064 chr9 141213431 6586857 0.04664469203357859 0.5091668647944302 chr10 135534747 7509444 0.055406042850399094 0.6010486823430021 chr11 135006516 7116048 0.05270892258267001 0.5012673937672663 chr12 133851895 7049195 0.05266414046659556 0.4808932216359185 chr13 115169878 4994376 0.04336529730456083 0.4146261058890823 chr14 107349540 4799818 0.04471205000040056 0.46215196460326957 chr15 102531392 4443698 0.043339877800547176 0.41252091916404415 chr16 90354753 4472922 0.04950400340311926 0.6051912608926753 chr17 81195210 4051334 0.0498962192474162 0.46284551737081875 chr18 78077248 4242143 0.05433263990042272 0.7181994597156233 chr19 59128983 3011666 0.05093383730276572 0.732828981236788 chr20 63025520 3335964 0.05293036852373451 0.47937401978181926 chr21 48129895 2046089 0.042511811006444127 0.45081031863417487 chr22 51304566 1857642 0.03620812229461214 0.4075376241566451 chrMT 16571 148863 8.983344396837849 9.510278269828483 chrX 155270560 4938970 0.0318087987832336 0.38592584324284757 chrY 59373566 1387339 0.023366273806090743 0.8340946568805295