BamQC report ----------------------------------- >>>>>>> Input bam file = SRR054616.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 18,484,340 number of mapped reads = 14,552,704 (78.73%) number of supplementary alignments = 1,078 (0.01%) number of secondary alignments = 0 number of mapped bases = 683,991,758 bp number of sequenced bases = 683,840,082 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,821,278 duplication rate = 13.84% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0296 >>>>>>> ACTG content number of A's = 201,987,533 bp (29.54%) number of C's = 134,503,202 bp (19.67%) number of T's = 202,093,646 bp (29.55%) number of G's = 145,182,008 bp (21.23%) number of N's = 73,693 bp (0.01%) GC percentage = 40.9% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 3,201,967 number of insertions = 32,686 mapped reads with insertion percentage = 0.22% number of deletions = 100,549 mapped reads with deletion percentage = 0.69% homopolymer indels = 45.35% >>>>>>> Coverage mean coverageData = 0.2209X std coverageData = 1.2837X There is a 9.64% of reference with a coverageData >= 1X There is a 3.96% of reference with a coverageData >= 2X There is a 2.24% of reference with a coverageData >= 3X There is a 1.44% of reference with a coverageData >= 4X There is a 0.99% of reference with a coverageData >= 5X There is a 0.72% of reference with a coverageData >= 6X There is a 0.53% of reference with a coverageData >= 7X There is a 0.41% of reference with a coverageData >= 8X There is a 0.32% of reference with a coverageData >= 9X There is a 0.26% of reference with a coverageData >= 10X There is a 0.21% of reference with a coverageData >= 11X There is a 0.17% of reference with a coverageData >= 12X There is a 0.14% of reference with a coverageData >= 13X There is a 0.12% of reference with a coverageData >= 14X There is a 0.1% of reference with a coverageData >= 15X There is a 0.09% of reference with a coverageData >= 16X There is a 0.07% of reference with a coverageData >= 17X There is a 0.06% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% 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 62653487 0.251367425880957 1.584728043827014 chr2 243199373 57533719 0.23657017816406953 1.388691748799702 chr3 198022430 50637644 0.2557167084557037 1.2930548591707711 chr4 191154276 41068106 0.21484272734762155 1.1868107160860624 chr5 180915260 33933028 0.18756310551138694 1.022264071256471 chr6 171115067 33072696 0.19327752126000686 1.2001035251739713 chr7 159138663 45061638 0.28315958642935185 1.5543493147097036 chr8 146364022 35551079 0.24289493083211391 1.334795270442434 chr9 141213431 33629199 0.23814447933072316 1.3019292355533887 chr10 135534747 29735373 0.21939298709872532 1.2970257428405825 chr11 135006516 30838541 0.22842261183897228 1.2662003625037916 chr12 133851895 27332171 0.20419711652195885 1.1109722863488833 chr13 115169878 20653512 0.17933084899160873 1.0505358585305722 chr14 107349540 13796113 0.12851580919676042 0.9970829955281806 chr15 102531392 19082518 0.18611390743627085 1.0349055366095654 chr16 90354753 19349957 0.2141553859374725 1.2465045461164335 chr17 81195210 13328631 0.16415538552089465 0.9589876666958268 chr18 78077248 26821888 0.3435301408164386 1.742944768325058 chr19 59128983 13070812 0.22105592446939262 1.4213936626204762 chr20 63025520 13158989 0.208788265451836 1.1545594624673492 chr21 48129895 7589550 0.15768889585152845 1.1322760163632295 chr22 51304566 6649757 0.12961335644082828 0.8201831247306355 chrMT 16571 33388 2.014845211514091 5.714996029617101 chrX 155270560 47761628 0.3076026002611184 1.520652891657132 chrY 59373566 1648334 0.027762085235035403 0.4682911203592998