BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006442.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 1,260,768 number of mapped reads = 1,170,499 (92.84%) number of supplementary alignments = 3,768 (0.3%) number of secondary alignments = 0 number of mapped bases = 64,536,666 bp number of sequenced bases = 64,514,986 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 27,231 duplication rate = 1.7% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5292 >>>>>>> ACTG content number of A's = 17,896,441 bp (27.74%) number of C's = 13,717,577 bp (21.26%) number of T's = 18,546,777 bp (28.75%) number of G's = 14,352,824 bp (22.25%) number of N's = 1,367 bp (0%) GC percentage = 43.51% >>>>>>> Mismatches and indels general error rate = 0.0044 number of mismatches = 274,900 number of insertions = 4,305 mapped reads with insertion percentage = 0.37% number of deletions = 12,777 mapped reads with deletion percentage = 1.09% homopolymer indels = 43.03% >>>>>>> Coverage mean coverageData = 0.0208X std coverageData = 0.2678X There is a 1.8% of reference with a coverageData >= 1X There is a 0.21% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 5185203 0.02080316983442942 0.23488048008868198 chr2 243199373 5531124 0.022743167187359484 0.20218972992829912 chr3 198022430 4249904 0.021461730370645388 0.16363637401184328 chr4 191154276 4316371 0.022580562100530777 0.18290366769888056 chr5 180915260 3789644 0.020947066599025423 0.16228960500305498 chr6 171115067 3767717 0.022018616280002977 0.17156814100371717 chr7 159138663 3728279 0.023427864289647826 0.20337256855288133 chr8 146364022 3260317 0.022275399073141074 0.901733988750869 chr9 141213431 2760840 0.019550831535280803 0.16468735815353172 chr10 135534747 3027054 0.02233415465039382 0.2168027768891066 chr11 135006516 2779220 0.020585821205844613 0.16926579279847065 chr12 133851895 3017993 0.022547256428457736 0.16962506826132107 chr13 115169878 1882282 0.01634352690726997 0.14297655387855035 chr14 107349540 1943545 0.018104828395165924 0.1538584619019386 chr15 102531392 1779374 0.017354431314070135 0.14776920683593509 chr16 90354753 2043931 0.02262117854497372 0.18219566917331667 chr17 81195210 1979630 0.02438111804871248 0.1841997783548355 chr18 78077248 1670616 0.02139696317165277 0.1954703129995013 chr19 59128983 1439016 0.02433689752451856 0.21126858454144753 chr20 63025520 1420971 0.022545962333987882 0.17292870631807308 chr21 48129895 1227703 0.02550811714839602 0.19497480118347588 chr22 51304566 830009 0.016178072727483943 0.15734400158881565 chrMT 16571 264723 15.975076941645042 9.08562356670416 chrX 155270560 2037683 0.01312343434582834 0.12956203833301677 chrY 59373566 603517 0.010164742336682287 0.16714641058729535