BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084285.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,501,055 number of mapped reads = 2,237,913 (89.48%) number of supplementary alignments = 15,991 (0.64%) number of secondary alignments = 0 number of mapped bases = 146,696,071 bp number of sequenced bases = 146,646,787 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 70,707 duplication rate = 2.64% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0627 >>>>>>> ACTG content number of A's = 40,860,700 bp (27.86%) number of C's = 28,289,691 bp (19.29%) number of T's = 44,656,855 bp (30.45%) number of G's = 32,661,124 bp (22.27%) number of N's = 178,417 bp (0.12%) GC percentage = 41.56% >>>>>>> Mismatches and indels general error rate = 0.0105 number of mismatches = 1,519,218 number of insertions = 11,184 mapped reads with insertion percentage = 0.5% number of deletions = 31,106 mapped reads with deletion percentage = 1.38% homopolymer indels = 46.6% >>>>>>> Coverage mean coverageData = 0.0474X std coverageData = 0.3184X There is a 4.06% of reference with a coverageData >= 1X There is a 0.51% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% 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 14421476 0.05785933829228052 0.4929784615478274 chr2 243199373 13671075 0.05621344673450289 0.3777498414794274 chr3 198022430 9814864 0.049564405405993654 0.25567872378834805 chr4 191154276 6929108 0.03624877321603834 0.22077593026513326 chr5 180915260 7500405 0.04145811138319675 0.22921428190810247 chr6 171115067 7044377 0.041167485268845436 0.2577887482576462 chr7 159138663 8025583 0.05043138385547452 0.4443202715284012 chr8 146364022 7434747 0.05079627423739421 0.3076616236259706 chr9 141213431 5557401 0.039354620595543774 0.26241428246302406 chr10 135534747 10439920 0.07702762746146566 0.46155826882651607 chr11 135006516 8115505 0.060111950448376875 0.3198416507641452 chr12 133851895 7330200 0.05476351306046134 0.2663090879852359 chr13 115169878 3518937 0.030554317336343798 0.1973916985992289 chr14 107349540 4039227 0.03762686826604008 0.2237457210738901 chr15 102531392 3170098 0.030918316216754376 0.20525074155271955 chr16 90354753 3324346 0.0367921541437892 0.23384147986242412 chr17 81195210 4402864 0.054225661833992425 0.27395393574580645 chr18 78077248 3737518 0.0478694894574153 0.38822147601652784 chr19 59128983 3144795 0.05318533890562603 0.3788272766994059 chr20 63025520 3032631 0.048117508590171096 0.24948671581904716 chr21 48129895 1509839 0.03137008713607208 0.2062427776331113 chr22 51304566 1223808 0.023853783306538447 0.17427043382291232 chrMT 16571 33050 1.994448132279283 1.7832497785472763 chrX 155270560 8975863 0.05780788708432558 0.30029843113308635 chrY 59373566 298434 0.0050263782370760755 0.10030752606049609