BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818862.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 679,255 number of mapped reads = 667,658 (98.29%) number of supplementary alignments = 10,386 (1.53%) number of secondary alignments = 0 number of mapped bases = 61,788,553 bp number of sequenced bases = 61,750,422 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 90,383 duplication rate = 11.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.4549 >>>>>>> ACTG content number of A's = 17,863,049 bp (28.93%) number of C's = 13,505,846 bp (21.87%) number of T's = 17,473,049 bp (28.3%) number of G's = 12,907,563 bp (20.9%) number of N's = 915 bp (0%) GC percentage = 42.77% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 375,129 number of insertions = 8,183 mapped reads with insertion percentage = 1.18% number of deletions = 19,960 mapped reads with deletion percentage = 2.92% homopolymer indels = 39.81% >>>>>>> Coverage mean coverageData = 0.02X std coverageData = 0.2595X There is a 1.61% of reference with a coverageData >= 1X There is a 0.26% of reference with a coverageData >= 2X There is a 0.05% 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% 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 5948723 0.023866432011818338 0.33558746186709915 chr2 243199373 4678322 0.019236570975863496 0.3792092495771187 chr3 198022430 3685267 0.018610351362721888 0.16192809408271935 chr4 191154276 3062449 0.016020823933857488 0.17685997492673805 chr5 180915260 2714773 0.015005771210234007 0.148670491877684 chr6 171115067 2886414 0.016868263272222545 0.16015580040654273 chr7 159138663 5496974 0.03454203960479422 0.4926056069784106 chr8 146364022 5326517 0.036392256288229084 0.2540115639305619 chr9 141213431 2299602 0.016284584148373252 0.21014303495196493 chr10 135534747 2898557 0.021386080427036176 0.3473478839096989 chr11 135006516 2720743 0.020152679149204916 0.18263305664787238 chr12 133851895 2435974 0.018199025123999926 0.16063853142701798 chr13 115169878 1852800 0.016087539833983328 0.1489148680140362 chr14 107349540 1858706 0.01731452226064499 0.16229480347846492 chr15 102531392 1730064 0.016873505433340843 0.1546788574279865 chr16 90354753 1613406 0.017856348962627343 0.2894792880353237 chr17 81195210 1698423 0.020917773351408292 0.1907785726624799 chr18 78077248 1166005 0.01493399203824397 0.22846779821263472 chr19 59128983 1085831 0.018363769253396427 0.30133232997020787 chr20 63025520 2627499 0.04168944579909852 0.25068396180582414 chr21 48129895 503330 0.01045774149309904 0.13555458779052104 chr22 51304566 605738 0.011806707418595063 0.13802221717174742 chrMT 16571 182715 11.0261903325086 7.346009898212372 chrX 155270560 2472244 0.015922168374996524 0.1644507036863155 chrY 59373566 237477 0.003999709230872203 0.32941768663655296