BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818789.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 = 1,387,569 number of mapped reads = 1,351,323 (97.39%) number of supplementary alignments = 10,315 (0.74%) number of secondary alignments = 0 number of mapped bases = 91,881,774 bp number of sequenced bases = 91,844,741 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 615,334 duplication rate = 38.25% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.8048 >>>>>>> ACTG content number of A's = 26,045,662 bp (28.36%) number of C's = 18,685,073 bp (20.34%) number of T's = 27,151,731 bp (29.56%) number of G's = 19,956,666 bp (21.73%) number of N's = 5,609 bp (0.01%) GC percentage = 42.07% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 476,693 number of insertions = 12,027 mapped reads with insertion percentage = 0.88% number of deletions = 23,084 mapped reads with deletion percentage = 1.69% homopolymer indels = 39.83% >>>>>>> Coverage mean coverageData = 0.0297X std coverageData = 0.3884X There is a 1.39% of reference with a coverageData >= 1X There is a 0.66% of reference with a coverageData >= 2X There is a 0.36% of reference with a coverageData >= 3X There is a 0.21% of reference with a coverageData >= 4X There is a 0.12% of reference with a coverageData >= 5X There is a 0.07% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% 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 7512610 0.030140787492762153 0.52696875065108 chr2 243199373 8107159 0.03333544367320388 0.5522142020735639 chr3 198022430 6273971 0.031683133067299495 0.32913164815274193 chr4 191154276 6176319 0.0323106504821268 0.35617389242007375 chr5 180915260 5716850 0.03159960082969231 0.33859565954571247 chr6 171115067 5387185 0.03148282085527863 0.35156165739854695 chr7 159138663 4902985 0.03080951484429651 0.36558234407075413 chr8 146364022 4767712 0.03257434398734957 0.3673844565666081 chr9 141213431 4043041 0.02863071147956174 0.3582424869464742 chr10 135534747 4438842 0.03275058314013011 0.4090634253589909 chr11 135006516 4302691 0.031870246914600775 0.3580971835866354 chr12 133851895 4284033 0.03200577025823953 0.3432368133968588 chr13 115169878 3016253 0.02618959967987463 0.29996215214195365 chr14 107349540 2904189 0.027053576568656 0.3255799054406114 chr15 102531392 2661676 0.02595962024976702 0.3024319398903205 chr16 90354753 2719931 0.03010279935135233 0.3948436694877868 chr17 81195210 2486016 0.030617766737717655 0.3445820171228761 chr18 78077248 2444418 0.031307686459440785 0.42444592623243627 chr19 59128983 1792376 0.030312985427129704 0.46806872250144343 chr20 63025520 1971408 0.0312795197881747 0.3442263308804189 chr21 48129895 1205796 0.025052953055476227 0.3006823632151547 chr22 51304566 1069724 0.02085046387489176 0.295193448358778 chrMT 16571 30054 1.8136503530263715 2.9290594709985056 chrX 155270560 2816128 0.01813690888987584 0.2605143143940337 chrY 59373566 850407 0.014322990133353284 0.45249216262012765