BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094030.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 480,220 number of mapped reads = 447,555 (93.2%) number of supplementary alignments = 18,031 (3.75%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 225,032 number of mapped paired reads (second in pair) = 222,523 number of mapped paired reads (both in pair) = 441,178 number of mapped paired reads (singletons) = 6,377 number of mapped bases = 58,613,890 bp number of sequenced bases = 57,484,485 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 419,241 duplication rate = 43.96% >>>>>>> Insert size mean insert size = 337,507.9025 std insert size = 5,511,759.3833 median insert size = 175 >>>>>>> Mapping quality mean mapping quality = 44.2336 >>>>>>> ACTG content number of A's = 16,028,877 bp (27.88%) number of C's = 12,746,984 bp (22.17%) number of T's = 15,559,962 bp (27.07%) number of G's = 13,148,149 bp (22.87%) number of N's = 513 bp (0%) GC percentage = 45.05% >>>>>>> Mismatches and indels general error rate = 0.037 number of mismatches = 2,040,545 number of insertions = 36,827 mapped reads with insertion percentage = 8.1% number of deletions = 150,393 mapped reads with deletion percentage = 32.5% homopolymer indels = 28.44% >>>>>>> Coverage mean coverageData = 0.0189X std coverageData = 7.8593X There is a 0.03% of reference with a coverageData >= 1X There is a 0.02% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% 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 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% 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 843439 0.003383899292270971 1.0249726124666299 chr2 243199373 1605065 0.0065997908637700315 1.6748977372826612 chr3 198022430 1071680 0.005411912175807559 1.940391580054416 chr4 191154276 681116 0.00356317428128053 1.0684518679272381 chr5 180915260 819640 0.00453051887386393 1.6306457693554617 chr6 171115067 997828 0.005831327524185816 2.5515241406096747 chr7 159138663 1370591 0.008612558219117375 1.9577732804592405 chr8 146364022 1511721 0.01032850135807282 3.90593544493683 chr9 141213431 1074223 0.007607088025500917 2.7263832290500933 chr10 135534747 1423220 0.010500775863771673 3.5748510937860325 chr11 135006516 1304998 0.009666185297308168 3.023673954018574 chr12 133851895 1461590 0.01091945691168586 3.479851764982411 chr13 115169878 1945328 0.016890944349181303 5.8449482684870295 chr14 107349540 524421 0.004885172307212495 1.3773398260759704 chr15 102531392 438776 0.004279430830315851 1.6207500585342682 chr16 90354753 451600 0.00499807685822571 1.852400701250622 chr17 81195210 1012344 0.012468026131098127 3.243172460902734 chr18 78077248 355759 0.004556500249598961 1.2579944967269785 chr19 59128983 379396 0.006416413419456242 1.0793029627325887 chr20 63025520 246305 0.003908020116295748 1.1460352026307004 chr21 48129895 215897 0.0044857151672572735 0.5637974201488598 chr22 51304566 269192 0.005246940399028032 0.7809517579269322 chrMT 16571 10838209 654.0467684509082 2796.4291562292237 chrX 155270560 27234840 0.17540247165979178 15.328443154012781 chrY 59373566 536712 0.00903957832008945 1.7979101385494622