BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081238.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,421,947 number of mapped reads = 2,124,532 (87.72%) number of supplementary alignments = 26,522 (1.1%) number of secondary alignments = 0 number of mapped bases = 138,271,044 bp number of sequenced bases = 138,219,818 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 98,783 duplication rate = 3.83% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2984 >>>>>>> ACTG content number of A's = 39,322,939 bp (28.45%) number of C's = 26,572,596 bp (19.22%) number of T's = 42,515,953 bp (30.76%) number of G's = 29,790,548 bp (21.55%) number of N's = 17,782 bp (0.01%) GC percentage = 40.78% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 1,262,381 number of insertions = 10,257 mapped reads with insertion percentage = 0.48% number of deletions = 31,326 mapped reads with deletion percentage = 1.46% homopolymer indels = 47.96% >>>>>>> Coverage mean coverageData = 0.0447X std coverageData = 0.3532X There is a 3.64% of reference with a coverageData >= 1X There is a 0.61% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.03% 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% 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 15666337 0.06285375313066924 0.6376461279183183 chr2 243199373 9300434 0.03824201471111523 0.35370123446874535 chr3 198022430 9742153 0.049197219729098365 0.26745099093545055 chr4 191154276 6960573 0.03641337847969459 0.22988419341768515 chr5 180915260 7299470 0.04034745327729679 0.2377943787305903 chr6 171115067 8477505 0.0495427150199462 0.2944444469808073 chr7 159138663 9416601 0.059172301830888195 0.4682249309580023 chr8 146364022 8511052 0.058149891508174054 0.3938260698643691 chr9 141213431 3081355 0.021820551899202845 0.23165184538585634 chr10 135534747 5733264 0.04230106394783029 0.40354723438001194 chr11 135006516 8202753 0.06075820073751107 0.478266302364266 chr12 133851895 4403194 0.03289601540568402 0.21643721698221446 chr13 115169878 3259535 0.028301974931327096 0.19980617336062825 chr14 107349540 5277151 0.049158580465272605 0.27163323123930216 chr15 102531392 2734650 0.026671343738315773 0.19623572024392721 chr16 90354753 5032550 0.05569767868216075 0.28905470485776047 chr17 81195210 2491939 0.03069071439066418 0.2464267966397329 chr18 78077248 3880855 0.049705325167198514 0.412059990557111 chr19 59128983 4289007 0.07253645813593648 0.49741193215126783 chr20 63025520 2962082 0.046998136627829486 0.25923922194571153 chr21 48129895 2197745 0.045662784013968866 0.2606192204087496 chr22 51304566 1035085 0.02017529979690307 0.16469467238253235 chrMT 16571 14770 0.8913161547281395 1.1530424943706434 chrX 155270560 7966983 0.0513103256663723 0.2971209445930982 chrY 59373566 334001 0.005625415862675319 0.10650313355156317