BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082322.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 = 3,006,277 number of mapped reads = 2,709,124 (90.12%) number of supplementary alignments = 25,858 (0.86%) number of secondary alignments = 0 number of mapped bases = 183,400,679 bp number of sequenced bases = 183,336,214 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 116,837 duplication rate = 3.23% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.873 >>>>>>> ACTG content number of A's = 52,141,030 bp (28.44%) number of C's = 33,949,963 bp (18.52%) number of T's = 57,656,050 bp (31.45%) number of G's = 39,585,324 bp (21.59%) number of N's = 3,847 bp (0%) GC percentage = 40.11% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 1,531,091 number of insertions = 14,596 mapped reads with insertion percentage = 0.53% number of deletions = 40,170 mapped reads with deletion percentage = 1.47% homopolymer indels = 47.76% >>>>>>> Coverage mean coverageData = 0.0592X std coverageData = 0.5207X There is a 5.05% of reference with a coverageData >= 1X There is a 0.64% of reference with a coverageData >= 2X There is a 0.1% 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 0.01% 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 14394627 0.05775161940318696 0.9472722975328308 chr2 243199373 15851713 0.06517990899590025 0.6005128176539705 chr3 198022430 12543814 0.06334542001125833 0.2839195432329434 chr4 191154276 12422045 0.06498439511758555 0.30157954908373885 chr5 180915260 11592890 0.06407911637746866 0.2888376226115355 chr6 171115067 10935150 0.06390524336468863 0.35413439327534413 chr7 159138663 10200040 0.06409529782212635 0.6768275084174027 chr8 146364022 9473620 0.06472642573323108 0.9896340173427086 chr9 141213431 7729920 0.0547392690996935 0.44160579228816 chr10 135534747 8437243 0.062251512521729946 0.4279089923752736 chr11 135006516 8276541 0.061304752135074726 0.4120598944663517 chr12 133851895 8324413 0.06219122261959758 0.2894199153725948 chr13 115169878 6106288 0.05301983562056044 0.2591911754155465 chr14 107349540 5588550 0.05205937538251212 0.2792408359713344 chr15 102531392 5127859 0.05001257566073033 0.26075406573982074 chr16 90354753 4799050 0.053113420607768136 0.2914451980778673 chr17 81195210 4394748 0.05412570519861948 0.3007615503166418 chr18 78077248 5070385 0.06494062137026141 0.8471586298298992 chr19 59128983 3102173 0.05246450797234243 0.7134553059807962 chr20 63025520 3509816 0.05568880669290789 0.2746847549160202 chr21 48129895 2365147 0.0491409133554104 0.26849352080031874 chr22 51304566 1782105 0.03473579719980479 0.20677532433484225 chrMT 16571 12308 0.7427433468106934 1.045976204777338 chrX 155270560 10921807 0.07034048824194361 0.34648708461068634 chrY 59373566 438427 0.0073842120245902025 0.1632224399436314