BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549099.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 11,836,164 number of mapped reads = 10,094,183 (85.28%) number of secondary alignments = 0 number of mapped bases = 400,411,212 bp number of sequenced bases = 400,373,707 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 482,888 duplication rate = 3.58% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.0367 >>>>>>> ACTG content number of A's = 120,720,650 bp (30.15%) number of C's = 78,645,495 bp (19.64%) number of T's = 122,027,179 bp (30.48%) number of G's = 78,978,654 bp (19.73%) number of N's = 1,729 bp (0%) GC percentage = 39.37% >>>>>>> Mismatches and indels general error rate = 0.003 number of mismatches = 1,200,789 number of insertions = 10,086 mapped reads with insertion percentage = 0.1% number of deletions = 30,177 mapped reads with deletion percentage = 0.3% homopolymer indels = 46.39% >>>>>>> Coverage mean coverageData = 0.1293X std coverageData = 0.8639X There is a 9.94% of reference with a coverageData >= 1X There is a 2.09% of reference with a coverageData >= 2X There is a 0.5% of reference with a coverageData >= 3X There is a 0.14% of reference with a coverageData >= 4X There is a 0.05% 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 0.01% 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 31442615 0.12614859242416893 1.742266992049568 chr2 243199373 35232477 0.14487075589623333 0.7563899955879807 chr3 198022430 29132939 0.14711938945502284 0.4771950018970024 chr4 191154276 28859283 0.1509737768042395 0.5011034444192598 chr5 180915260 26472335 0.14632450021076165 0.4893336828193057 chr6 171115067 24889114 0.14545249834720866 0.557417522608772 chr7 159138663 22896064 0.14387493000365348 1.2345033606938565 chr8 146364022 21428000 0.14640209873434606 1.1717030298347961 chr9 141213431 17055391 0.1207773997078224 0.7334035511093252 chr10 135534747 18409447 0.13582824631679136 0.7170984822377179 chr11 135006516 18728206 0.13872075626334954 0.7348809226636672 chr12 133851895 18632081 0.139199232106501 0.496815073616451 chr13 115169878 14006480 0.12161582736069235 0.42519751264843075 chr14 107349540 12382592 0.11534834709119388 0.5907798410448839 chr15 102531392 11399869 0.11118418249895602 0.4082649911240255 chr16 90354753 10023572 0.11093574678910362 0.49639824076476646 chr17 81195210 8791811 0.10827992193135531 0.45923624486308134 chr18 78077248 11240433 0.14396553782223473 1.6795414161088518 chr19 59128983 5874211 0.09934571342111533 1.3585964394495307 chr20 63025520 7489546 0.11883354552251216 0.47087906281717495 chr21 48129895 5269380 0.10948247445792267 0.505685289641833 chr22 51304566 3490044 0.06802599207251846 0.3384910781993503 chrMT 16571 95144 5.741596765433589 7.074486593633812 chrX 155270560 13992916 0.09011956935042933 0.507605441375686 chrY 59373566 3177262 0.05351307347785039 0.42419556315359636