BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063540.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 4,563,249 number of mapped reads = 4,263,294 (93.43%) number of supplementary alignments = 35,184 (0.77%) number of secondary alignments = 0 number of mapped bases = 273,154,964 bp number of sequenced bases = 273,051,683 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 724,143 duplication rate = 13.74% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3417 >>>>>>> ACTG content number of A's = 70,050,190 bp (25.65%) number of C's = 49,121,822 bp (17.99%) number of T's = 89,158,906 bp (32.65%) number of G's = 64,690,290 bp (23.69%) number of N's = 30,475 bp (0.01%) GC percentage = 41.68% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 1,432,910 number of insertions = 17,283 mapped reads with insertion percentage = 0.4% number of deletions = 58,960 mapped reads with deletion percentage = 1.37% homopolymer indels = 44.36% >>>>>>> Coverage mean coverageData = 0.0882X std coverageData = 0.9526X There is a 5.73% of reference with a coverageData >= 1X There is a 1.85% of reference with a coverageData >= 2X There is a 0.65% of reference with a coverageData >= 3X There is a 0.24% of reference with a coverageData >= 4X There is a 0.1% 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 0.01% 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 29166761 0.11701780674801207 1.9553226657702607 chr2 243199373 28223096 0.11604921366306319 1.8096439619810212 chr3 198022430 14105554 0.07123210234315375 0.3874299565141099 chr4 191154276 15888300 0.08311768029714386 0.4485131157972934 chr5 180915260 15176076 0.08388499676588917 0.4201864417090884 chr6 171115067 16815467 0.09826993785415752 0.6513461155304212 chr7 159138663 25606713 0.16090818231896292 1.0217722934125164 chr8 146364022 8517320 0.05819271624006069 0.8910854355835119 chr9 141213431 9758010 0.06910114661827033 0.6875319940835263 chr10 135534747 14284291 0.10539209550448343 0.6304168633731082 chr11 135006516 14161222 0.1048928779111669 0.6388800076036416 chr12 133851895 11604095 0.08669354288932554 0.4601376616275766 chr13 115169878 7559255 0.06563569512507428 0.4365380713569255 chr14 107349540 5309374 0.04945874942733802 0.3750989808305082 chr15 102531392 4373632 0.04265651635744885 0.3493177060521634 chr16 90354753 4625509 0.05119275795043123 0.3808833675636654 chr17 81195210 7218609 0.08890437009769418 0.4840565333042091 chr18 78077248 5677133 0.07271174568038054 1.2897308712548003 chr19 59128983 4106942 0.06945734209566906 1.2169721660745318 chr20 63025520 3921137 0.0622150678011066 0.4061532557759574 chr21 48129895 5001911 0.10392524230522422 0.4896280675941708 chr22 51304566 2817060 0.054908563109178236 0.32855179828943815 chrMT 16571 255022 15.389656629050751 9.57898681951771 chrX 155270560 18131448 0.11677325051188069 0.596826084757687 chrY 59373566 851027 0.014333432490815862 0.42693838783230303