BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472449.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 17,164,478 number of mapped reads = 17,010,403 (99.1%) number of supplementary alignments = 66,483 (0.39%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,528,150 number of mapped paired reads (second in pair) = 8,482,253 number of mapped paired reads (both in pair) = 16,922,726 number of mapped paired reads (singletons) = 87,677 number of mapped bases = 1,664,405,393 bp number of sequenced bases = 1,664,216,771 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,559,620 duplication rate = 47.09% >>>>>>> Insert size mean insert size = 18,664.8723 std insert size = 1,357,234.4095 median insert size = 208 >>>>>>> Mapping quality mean mapping quality = 54.8666 >>>>>>> ACTG content number of A's = 457,485,480 bp (27.49%) number of C's = 375,969,034 bp (22.59%) number of T's = 458,251,508 bp (27.54%) number of G's = 372,304,041 bp (22.37%) number of N's = 206,708 bp (0.01%) GC percentage = 44.96% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 8,951,295 number of insertions = 102,492 mapped reads with insertion percentage = 0.6% number of deletions = 80,482 mapped reads with deletion percentage = 0.47% homopolymer indels = 46.99% >>>>>>> Coverage mean coverageData = 0.5377X std coverageData = 16.6456X There is a 4.81% of reference with a coverageData >= 1X There is a 2.12% of reference with a coverageData >= 2X There is a 0.87% of reference with a coverageData >= 3X There is a 0.65% of reference with a coverageData >= 4X There is a 0.49% of reference with a coverageData >= 5X There is a 0.44% of reference with a coverageData >= 6X There is a 0.41% of reference with a coverageData >= 7X There is a 0.39% of reference with a coverageData >= 8X There is a 0.37% of reference with a coverageData >= 9X There is a 0.35% of reference with a coverageData >= 10X There is a 0.34% of reference with a coverageData >= 11X There is a 0.33% of reference with a coverageData >= 12X There is a 0.32% of reference with a coverageData >= 13X There is a 0.31% of reference with a coverageData >= 14X There is a 0.31% of reference with a coverageData >= 15X There is a 0.3% of reference with a coverageData >= 16X There is a 0.29% of reference with a coverageData >= 17X There is a 0.29% of reference with a coverageData >= 18X There is a 0.28% of reference with a coverageData >= 19X There is a 0.27% of reference with a coverageData >= 20X There is a 0.27% of reference with a coverageData >= 21X There is a 0.26% of reference with a coverageData >= 22X There is a 0.26% of reference with a coverageData >= 23X There is a 0.25% of reference with a coverageData >= 24X There is a 0.25% of reference with a coverageData >= 25X There is a 0.24% of reference with a coverageData >= 26X There is a 0.24% of reference with a coverageData >= 27X There is a 0.24% of reference with a coverageData >= 28X There is a 0.23% of reference with a coverageData >= 29X There is a 0.23% of reference with a coverageData >= 30X There is a 0.23% of reference with a coverageData >= 31X There is a 0.22% of reference with a coverageData >= 32X There is a 0.22% of reference with a coverageData >= 33X There is a 0.22% of reference with a coverageData >= 34X There is a 0.21% of reference with a coverageData >= 35X There is a 0.21% of reference with a coverageData >= 36X There is a 0.21% of reference with a coverageData >= 37X There is a 0.2% of reference with a coverageData >= 38X There is a 0.2% of reference with a coverageData >= 39X There is a 0.2% of reference with a coverageData >= 40X There is a 0.2% of reference with a coverageData >= 41X There is a 0.19% of reference with a coverageData >= 42X There is a 0.19% of reference with a coverageData >= 43X There is a 0.19% of reference with a coverageData >= 44X There is a 0.19% of reference with a coverageData >= 45X There is a 0.18% of reference with a coverageData >= 46X There is a 0.18% of reference with a coverageData >= 47X There is a 0.18% of reference with a coverageData >= 48X There is a 0.18% of reference with a coverageData >= 49X There is a 0.18% of reference with a coverageData >= 50X There is a 0.17% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 161197685 0.6467293214888319 18.557822472906253 chr2 243199373 133393759 0.5484954889254587 18.46005385914398 chr3 198022430 129295035 0.6529312613727647 16.12354172325123 chr4 191154276 48065075 0.25144650700882043 9.819920376103005 chr5 180915260 94563261 0.5226936688480562 24.72929387487384 chr6 171115067 142418343 0.8322957498535182 18.84066112335548 chr7 159138663 91190958 0.5730283029963623 15.386017501988482 chr8 146364022 150317081 1.027008406478472 25.639893651590477 chr9 141213431 44222596 0.3131614017649638 10.784897156177482 chr10 135534747 39752086 0.2932981163863463 10.921176510566548 chr11 135006516 60531986 0.44836344047275467 14.368651779127458 chr12 133851895 87334253 0.6524693057203261 15.8995643701175 chr13 115169878 54199724 0.4706067675091225 13.72305442295803 chr14 107349540 26954069 0.2510869538891364 8.020270116471595 chr15 102531392 28677881 0.27969854344706446 8.319411703298599 chr16 90354753 72063643 0.7975633888346748 19.69716393459888 chr17 81195210 82477188 1.0157888377898154 23.048423143151886 chr18 78077248 9301078 0.11912661163467236 4.175807672190114 chr19 59128983 32721035 0.5533840316516183 12.473590908473254 chr20 63025520 63983179 1.0151947814155282 29.854495145886883 chr21 48129895 13091581 0.2720051851349354 13.42249333591359 chr22 51304566 15885115 0.30962380619300045 9.534534305441243 chrMT 16571 3406 0.2055397984430632 0.5521592992026394 chrX 155270560 82392783 0.5306400839927414 12.786256292014343 chrY 59373566 372593 0.006275402087184725 0.6177418640753244