BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013350.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 = 1,809,804 number of mapped reads = 1,537,667 (84.96%) number of supplementary alignments = 24,188 (1.34%) number of secondary alignments = 0 number of mapped bases = 102,007,551 bp number of sequenced bases = 101,961,563 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 310,453 duplication rate = 12.75% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2252 >>>>>>> ACTG content number of A's = 28,756,695 bp (28.2%) number of C's = 18,696,763 bp (18.34%) number of T's = 32,632,312 bp (32%) number of G's = 21,863,550 bp (21.44%) number of N's = 12,243 bp (0.01%) GC percentage = 39.78% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 788,282 number of insertions = 7,656 mapped reads with insertion percentage = 0.49% number of deletions = 26,892 mapped reads with deletion percentage = 1.73% homopolymer indels = 46.57% >>>>>>> Coverage mean coverageData = 0.033X std coverageData = 0.5672X There is a 1.14% of reference with a coverageData >= 1X There is a 0.66% of reference with a coverageData >= 2X There is a 0.45% of reference with a coverageData >= 3X There is a 0.31% of reference with a coverageData >= 4X There is a 0.21% of reference with a coverageData >= 5X There is a 0.15% of reference with a coverageData >= 6X There is a 0.1% of reference with a coverageData >= 7X There is a 0.07% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% 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 0.01% of reference with a coverageData >= 15X There is a 0.01% 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 6244286 0.025052238485696692 1.1956657688230576 chr2 243199373 8495992 0.03493426769648785 0.5196685725276009 chr3 198022430 4748218 0.023978182673548648 0.3520106126274625 chr4 191154276 3480136 0.01820590191767408 0.3018145408483373 chr5 180915260 4298323 0.023758764186061473 0.3435182279531079 chr6 171115067 4946257 0.02890602847965457 0.39487818256276247 chr7 159138663 5982722 0.03759439652952218 0.5282830175387798 chr8 146364022 5075886 0.03467987508569558 0.5763926860274534 chr9 141213431 3697208 0.026181702220662 0.42316631306225116 chr10 135534747 10524692 0.07765309068677421 0.722201809128101 chr11 135006516 4706143 0.03485863600835385 0.4452369491392527 chr12 133851895 4728707 0.035327904771165174 0.42807916778166394 chr13 115169878 2811453 0.0244113569348402 0.3556432266903064 chr14 107349540 3360472 0.03130401862923679 0.4231487825226583 chr15 102531392 5016597 0.04892742507582458 0.5074702458735552 chr16 90354753 2767751 0.030632046550998816 0.40320555184601053 chr17 81195210 1647273 0.020287810081407513 0.3218332497303098 chr18 78077248 4129386 0.05288846758533292 0.8532594454472723 chr19 59128983 1527959 0.02584111754467348 0.6920392916044313 chr20 63025520 1228065 0.01948520218476579 0.3137354964363132 chr21 48129895 2438652 0.05066813463856507 0.5127705257929978 chr22 51304566 774300 0.01509222395527135 0.2594931554193732 chrMT 16571 45266 2.7316396113692596 3.805250884529748 chrX 155270560 9053044 0.058304961352622156 0.5715434624090389 chrY 59373566 278763 0.0046950691828077165 0.13849882739180575