BamQC report ----------------------------------- >>>>>>> Input bam file = SRR054213.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 = 7,429,097 number of mapped reads = 6,005,563 (80.84%) number of supplementary alignments = 243 (0%) number of secondary alignments = 0 number of mapped bases = 282,662,927 bp number of sequenced bases = 282,603,279 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,237,304 duplication rate = 15.5% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1767 >>>>>>> ACTG content number of A's = 84,305,250 bp (29.83%) number of C's = 55,297,816 bp (19.57%) number of T's = 83,808,557 bp (29.66%) number of G's = 59,133,229 bp (20.92%) number of N's = 58,427 bp (0.02%) GC percentage = 40.49% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 1,492,344 number of insertions = 11,721 mapped reads with insertion percentage = 0.19% number of deletions = 39,656 mapped reads with deletion percentage = 0.66% homopolymer indels = 46.68% >>>>>>> Coverage mean coverageData = 0.0913X std coverageData = 0.736X There is a 4.4% of reference with a coverageData >= 1X There is a 1.73% of reference with a coverageData >= 2X There is a 0.96% of reference with a coverageData >= 3X There is a 0.59% of reference with a coverageData >= 4X There is a 0.38% of reference with a coverageData >= 5X There is a 0.26% of reference with a coverageData >= 6X There is a 0.18% of reference with a coverageData >= 7X There is a 0.13% of reference with a coverageData >= 8X There is a 0.1% of reference with a coverageData >= 9X There is a 0.07% of reference with a coverageData >= 10X There is a 0.06% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% 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% 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 23870903 0.09577068616410789 0.788861397987075 chr2 243199373 29671102 0.1220032010526606 0.830969805267908 chr3 198022430 18111574 0.09146223485895007 0.6329494150847812 chr4 191154276 13500146 0.07062434742500869 0.570065693504907 chr5 180915260 14053278 0.07767878729522319 0.5773942310739649 chr6 171115067 17122643 0.10006508076813599 0.7363980982714777 chr7 159138663 14682873 0.09226464972877144 1.3613277420242276 chr8 146364022 16492995 0.11268476210635972 0.7751276167333544 chr9 141213431 14879833 0.10537123058783268 0.7571622788277786 chr10 135534747 9633344 0.07107656311927155 0.6186401811577505 chr11 135006516 13420572 0.09940684640732451 0.7050345501280583 chr12 133851895 15122254 0.1129775114502488 0.7359861629794087 chr13 115169878 7698223 0.06684233007523026 0.5435794189793922 chr14 107349540 5394158 0.05024854321685961 0.5337509202480406 chr15 102531392 8272406 0.08068169015007619 0.5883253764928791 chr16 90354753 6882025 0.07616671809174222 0.6092306347538219 chr17 81195210 6414403 0.07899977104560725 0.5802739252009168 chr18 78077248 9002424 0.11530150243000369 0.8053585503702768 chr19 59128983 5679079 0.09604560592560843 0.7359778271005237 chr20 63025520 6043962 0.09589705884219599 0.6692982214582924 chr21 48129895 3503781 0.07279843432029096 0.6257930193214264 chr22 51304566 4274435 0.08331490417441598 0.6249404920619953 chrMT 16571 33811 2.040371733751735 3.7371635513993935 chrX 155270560 18253508 0.11755936218688205 0.7555785582462915 chrY 59373566 649195 0.010934074601481743 0.21535627650746816