BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548973.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 8,781,316 number of mapped reads = 3,870,953 (44.08%) number of secondary alignments = 0 number of mapped bases = 152,982,161 bp number of sequenced bases = 152,961,844 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 107,177 duplication rate = 1.95% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.8564 >>>>>>> ACTG content number of A's = 46,671,191 bp (30.51%) number of C's = 29,493,399 bp (19.28%) number of T's = 46,969,562 bp (30.71%) number of G's = 29,819,540 bp (19.49%) number of N's = 8,152 bp (0.01%) GC percentage = 38.78% >>>>>>> Mismatches and indels general error rate = 0.0031 number of mismatches = 474,363 number of insertions = 6,131 mapped reads with insertion percentage = 0.16% number of deletions = 16,268 mapped reads with deletion percentage = 0.42% homopolymer indels = 45.03% >>>>>>> Coverage mean coverageData = 0.0494X std coverageData = 0.373X There is a 4.17% of reference with a coverageData >= 1X There is a 0.57% of reference with a coverageData >= 2X There is a 0.1% 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 0.01% 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 12100716 0.04854838857151734 0.6390531312256812 chr2 243199373 13349301 0.054890359441839516 0.34927400802356523 chr3 198022430 10919751 0.05514401070626191 0.2712996681794119 chr4 191154276 10741465 0.05619264828792007 0.27868998902810854 chr5 180915260 9880923 0.05461630489324118 0.2734062862293082 chr6 171115067 9362834 0.05471659605521471 0.30407950005064777 chr7 159138663 8661190 0.054425428973221925 0.5336226185405559 chr8 146364022 8101911 0.055354525581430114 0.4999642178076629 chr9 141213431 6582623 0.04661470904987784 0.3258449382484591 chr10 135534747 7127157 0.05258545987472866 0.3231450477593966 chr11 135006516 7028976 0.05206397593431713 0.3580304320325162 chr12 133851895 7050502 0.052673904990287956 0.273686499560102 chr13 115169878 5220713 0.045330542071078686 0.2441130597804225 chr14 107349540 4835401 0.04504351858424358 0.2849747847085415 chr15 102531392 4384338 0.0427609331588905 0.2364665285929325 chr16 90354753 3980398 0.04405300073146124 0.25546734633693424 chr17 81195210 3722212 0.04584275353188938 0.2615365342451273 chr18 78077248 4218884 0.05403474261797752 0.5630593077087639 chr19 59128983 2539751 0.04295272590769911 0.5969642277557787 chr20 63025520 3007143 0.04771310097877812 0.2590643786880589 chr21 48129895 2037801 0.04233961033989374 0.25750065600618166 chr22 51304566 1508891 0.0294104622188988 0.2117128526081031 chrMT 16571 6386 0.3853720354836763 0.7041783355087987 chrX 155270560 5290276 0.03407133973111194 0.25040045507502634 chrY 59373566 1322618 0.022276209584581798 0.25563234235263693