BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548988.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 = 7,141,022 number of mapped reads = 3,189,115 (44.66%) number of secondary alignments = 0 number of mapped bases = 126,234,998 bp number of sequenced bases = 126,220,121 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 66,900 duplication rate = 1.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.0723 >>>>>>> ACTG content number of A's = 37,334,982 bp (29.58%) number of C's = 25,522,217 bp (20.22%) number of T's = 37,525,212 bp (29.73%) number of G's = 25,831,378 bp (20.47%) number of N's = 6,332 bp (0.01%) GC percentage = 40.69% >>>>>>> Mismatches and indels general error rate = 0.0029 number of mismatches = 358,466 number of insertions = 4,404 mapped reads with insertion percentage = 0.14% number of deletions = 11,890 mapped reads with deletion percentage = 0.37% homopolymer indels = 45.77% >>>>>>> Coverage mean coverageData = 0.0408X std coverageData = 0.3087X There is a 3.62% of reference with a coverageData >= 1X There is a 0.35% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 10124325 0.04061905627107745 0.5031667452139077 chr2 243199373 10860641 0.04465735608619353 0.3009433196475538 chr3 198022430 8719676 0.04403377940569662 0.23014790111518488 chr4 191154276 8553782 0.04474805470739247 0.23429243673098768 chr5 180915260 7953484 0.04396248276679369 0.2316899498414662 chr6 171115067 7451558 0.043547059476650295 0.2563076594315021 chr7 159138663 7287050 0.04579056944823019 0.4600726980515899 chr8 146364022 6432009 0.0439452873193113 0.44861537594672835 chr9 141213431 5556198 0.03934610157584798 0.2752611520824131 chr10 135534747 5848202 0.043149097404520186 0.2610179207355969 chr11 135006516 6104888 0.04521921001205601 0.2902495516952288 chr12 133851895 5934433 0.044335816089865594 0.23627851374911119 chr13 115169878 4350963 0.037778654241519646 0.21183015499361818 chr14 107349540 3987906 0.03714879448947802 0.2306388514146512 chr15 102531392 3978147 0.0387993074355218 0.21532577402710879 chr16 90354753 3576500 0.039582865109486824 0.23127235950692948 chr17 81195210 3189992 0.039287933364542074 0.23037421624253235 chr18 78077248 3372118 0.04318950893351159 0.43415109303330685 chr19 59128983 2349986 0.039743386081915195 0.4369164009687623 chr20 63025520 2872032 0.04556935032031469 0.2381135323605741 chr21 48129895 1647949 0.03423961344607131 0.2162614385889744 chr22 51304566 1468533 0.028623826581049335 0.19055787507018354 chrMT 16571 5073 0.3061372276869229 0.5761135112790603 chrX 155270560 4279629 0.02756239817773569 0.20815038439881117 chrY 59373566 329924 0.005556748941102847 0.10459079730571398