BamQC report ----------------------------------- >>>>>>> Input bam file = SRR054565.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 = 13,436,964 number of mapped reads = 10,557,169 (78.57%) number of supplementary alignments = 284 (0%) number of secondary alignments = 0 number of mapped bases = 499,959,843 bp number of sequenced bases = 499,859,122 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,690,397 duplication rate = 18.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4664 >>>>>>> ACTG content number of A's = 146,484,076 bp (29.31%) number of C's = 95,880,736 bp (19.18%) number of T's = 148,148,437 bp (29.64%) number of G's = 109,339,679 bp (21.87%) number of N's = 6,194 bp (0%) GC percentage = 41.06% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 2,371,176 number of insertions = 20,176 mapped reads with insertion percentage = 0.19% number of deletions = 67,305 mapped reads with deletion percentage = 0.64% homopolymer indels = 48.43% >>>>>>> Coverage mean coverageData = 0.1615X std coverageData = 1.1405X There is a 6.24% of reference with a coverageData >= 1X There is a 2.95% of reference with a coverageData >= 2X There is a 1.82% of reference with a coverageData >= 3X There is a 1.22% of reference with a coverageData >= 4X There is a 0.86% of reference with a coverageData >= 5X There is a 0.62% of reference with a coverageData >= 6X There is a 0.46% of reference with a coverageData >= 7X There is a 0.35% of reference with a coverageData >= 8X There is a 0.27% of reference with a coverageData >= 9X There is a 0.21% of reference with a coverageData >= 10X There is a 0.17% of reference with a coverageData >= 11X There is a 0.14% of reference with a coverageData >= 12X There is a 0.11% of reference with a coverageData >= 13X There is a 0.09% of reference with a coverageData >= 14X There is a 0.08% of reference with a coverageData >= 15X There is a 0.06% of reference with a coverageData >= 16X There is a 0.05% of reference with a coverageData >= 17X There is a 0.05% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% 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 0.01% 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% 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 43326770 0.17382813260874483 1.2562613689366713 chr2 243199373 53886861 0.22157483522788524 1.476217760431432 chr3 198022430 31576127 0.15945732511210978 1.0042063023705778 chr4 191154276 22784836 0.11919605711566714 0.853554090043074 chr5 180915260 24529309 0.13558452172580687 0.903162370111137 chr6 171115067 29712860 0.1736425700023248 1.1582488781974107 chr7 159138663 25543402 0.16051034687906107 1.417372962213617 chr8 146364022 29103722 0.19884478167728953 1.2725010387541067 chr9 141213431 25843360 0.18300922098550243 1.1822592738254176 chr10 135534747 16970447 0.12521104274463285 1.022169353423558 chr11 135006516 24874806 0.1842489291405757 1.2499883000041252 chr12 133851895 28160907 0.21038855669544312 1.208633628083131 chr13 115169878 12168388 0.10565599453009752 0.8060672898911871 chr14 107349540 9553760 0.0889967483791733 0.909808724946077 chr15 102531392 12363188 0.12057953919127519 0.8509992103284556 chr16 90354753 13644264 0.15100770625757784 0.9950976855934939 chr17 81195210 13915078 0.17137806528242244 1.0824896329711295 chr18 78077248 13767870 0.17633651739364584 1.2572570817289386 chr19 59128983 11391485 0.19265484407198413 1.3144015366467434 chr20 63025520 11634008 0.1845920192328441 1.1324360678182384 chr21 48129895 5629489 0.11696449784484259 0.9424907706850196 chr22 51304566 7765643 0.1513635842860458 0.9936116209834703 chrMT 16571 30018 1.8114778830486995 3.953604086127944 chrX 155270560 30642106 0.19734652853702594 1.2648257537238665 chrY 59373566 1141139 0.019219647342724876 0.3970159079180479