BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472375.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 = 19,418,368 number of mapped reads = 19,249,122 (99.13%) number of supplementary alignments = 62,703 (0.32%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,662,418 number of mapped paired reads (second in pair) = 9,586,704 number of mapped paired reads (both in pair) = 19,139,114 number of mapped paired reads (singletons) = 110,008 number of mapped bases = 1,883,003,832 bp number of sequenced bases = 1,882,804,095 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,097,583 duplication rate = 48.75% >>>>>>> Insert size mean insert size = 17,042.3909 std insert size = 1,303,846.5219 median insert size = 200 >>>>>>> Mapping quality mean mapping quality = 54.881 >>>>>>> ACTG content number of A's = 497,271,337 bp (26.41%) number of C's = 446,030,994 bp (23.69%) number of T's = 497,802,579 bp (26.44%) number of G's = 441,463,429 bp (23.45%) number of N's = 235,756 bp (0.01%) GC percentage = 47.14% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 9,675,554 number of insertions = 104,023 mapped reads with insertion percentage = 0.53% number of deletions = 81,389 mapped reads with deletion percentage = 0.42% homopolymer indels = 45.14% >>>>>>> Coverage mean coverageData = 0.6083X std coverageData = 16.898X There is a 5.12% of reference with a coverageData >= 1X There is a 2.3% of reference with a coverageData >= 2X There is a 0.93% of reference with a coverageData >= 3X There is a 0.7% of reference with a coverageData >= 4X There is a 0.52% of reference with a coverageData >= 5X There is a 0.47% of reference with a coverageData >= 6X There is a 0.43% of reference with a coverageData >= 7X There is a 0.41% of reference with a coverageData >= 8X There is a 0.39% of reference with a coverageData >= 9X There is a 0.38% of reference with a coverageData >= 10X There is a 0.37% of reference with a coverageData >= 11X There is a 0.36% of reference with a coverageData >= 12X There is a 0.35% of reference with a coverageData >= 13X There is a 0.34% of reference with a coverageData >= 14X There is a 0.33% of reference with a coverageData >= 15X There is a 0.32% of reference with a coverageData >= 16X There is a 0.32% of reference with a coverageData >= 17X There is a 0.31% of reference with a coverageData >= 18X There is a 0.3% of reference with a coverageData >= 19X There is a 0.3% of reference with a coverageData >= 20X There is a 0.29% of reference with a coverageData >= 21X There is a 0.29% of reference with a coverageData >= 22X There is a 0.28% of reference with a coverageData >= 23X There is a 0.28% of reference with a coverageData >= 24X There is a 0.27% of reference with a coverageData >= 25X There is a 0.27% of reference with a coverageData >= 26X There is a 0.27% of reference with a coverageData >= 27X There is a 0.26% of reference with a coverageData >= 28X There is a 0.26% of reference with a coverageData >= 29X There is a 0.25% of reference with a coverageData >= 30X There is a 0.25% of reference with a coverageData >= 31X There is a 0.25% of reference with a coverageData >= 32X There is a 0.24% of reference with a coverageData >= 33X There is a 0.24% of reference with a coverageData >= 34X There is a 0.24% of reference with a coverageData >= 35X There is a 0.24% of reference with a coverageData >= 36X There is a 0.23% of reference with a coverageData >= 37X There is a 0.23% of reference with a coverageData >= 38X There is a 0.23% of reference with a coverageData >= 39X There is a 0.22% of reference with a coverageData >= 40X There is a 0.22% of reference with a coverageData >= 41X There is a 0.22% of reference with a coverageData >= 42X There is a 0.22% of reference with a coverageData >= 43X There is a 0.21% of reference with a coverageData >= 44X There is a 0.21% of reference with a coverageData >= 45X There is a 0.21% of reference with a coverageData >= 46X There is a 0.21% of reference with a coverageData >= 47X There is a 0.2% of reference with a coverageData >= 48X There is a 0.2% of reference with a coverageData >= 49X There is a 0.2% of reference with a coverageData >= 50X There is a 0.2% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 177235237 0.7110723988928397 19.10548900084728 chr2 243199373 156396357 0.6430787837598578 18.68528665544422 chr3 198022430 118527472 0.5985557898668348 12.835538202091174 chr4 191154276 43209459 0.226044951251836 7.98554835676 chr5 180915260 68535452 0.37882626374358913 11.039728358443684 chr6 171115067 138200118 0.8076443554792285 17.645136561108913 chr7 159138663 164006120 1.0305862630000857 26.583810247950424 chr8 146364022 92947204 0.6350413354997856 18.003621135776847 chr9 141213431 69059226 0.48904148501285266 13.514946516027027 chr10 135534747 55509940 0.40956242755962796 14.247192687699506 chr11 135006516 55650966 0.4122094818001229 10.47458012959025 chr12 133851895 100875548 0.753635561155111 17.348897520415985 chr13 115169878 59735474 0.5186727210043585 16.31626458798647 chr14 107349540 40620101 0.37839101127028585 11.54117582291656 chr15 102531392 39405943 0.384330518013449 13.907347975330628 chr16 90354753 99504041 1.1012596205093936 27.25320489687818 chr17 81195210 95733371 1.1790519539268387 25.938897500951615 chr18 78077248 22186496 0.28416083517697754 8.867055628289418 chr19 59128983 51586254 0.8724360099344174 18.540756244319414 chr20 63025520 70331088 1.1159144422767158 24.575733075163257 chr21 48129895 10687571 0.2220568110526732 10.009174474421334 chr22 51304566 20534601 0.4002489953818146 12.107396885701052 chrMT 16571 29114 1.756924748053829 2.023426862037794 chrX 155270560 131980183 0.8500013331567813 18.984173441738015 chrY 59373566 516496 0.008699090096761243 0.7309284070028726