BamQC report ----------------------------------- >>>>>>> Input bam file = SRR053609.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 = 8,687,962 number of mapped reads = 5,498,803 (63.29%) number of supplementary alignments = 136 (0%) number of secondary alignments = 0 number of mapped bases = 258,159,954 bp number of sequenced bases = 258,108,246 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,451,512 duplication rate = 20.05% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2393 >>>>>>> ACTG content number of A's = 77,585,047 bp (30.06%) number of C's = 49,168,729 bp (19.05%) number of T's = 77,824,855 bp (30.15%) number of G's = 53,369,801 bp (20.68%) number of N's = 159,814 bp (0.06%) GC percentage = 39.73% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 2,284,673 number of insertions = 13,743 mapped reads with insertion percentage = 0.25% number of deletions = 36,198 mapped reads with deletion percentage = 0.66% homopolymer indels = 46.53% >>>>>>> Coverage mean coverageData = 0.0834X std coverageData = 0.8525X There is a 3.87% of reference with a coverageData >= 1X There is a 1.61% of reference with a coverageData >= 2X There is a 0.88% of reference with a coverageData >= 3X There is a 0.54% of reference with a coverageData >= 4X There is a 0.35% of reference with a coverageData >= 5X There is a 0.24% of reference with a coverageData >= 6X There is a 0.17% of reference with a coverageData >= 7X There is a 0.13% of reference with a coverageData >= 8X There is a 0.09% 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 0.04% 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 0.02% 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 0.01% 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 20265745 0.08130669812854749 0.738777419926855 chr2 243199373 22570694 0.09280736920320926 1.9397301690364512 chr3 198022430 17853118 0.09015704938071914 0.6549802063978318 chr4 191154276 17225486 0.09011300380222727 0.6787239695277504 chr5 180915260 16182929 0.08945032608084028 0.652324838497923 chr6 171115067 15454985 0.09031925283353336 0.7315415175220261 chr7 159138663 13872585 0.08717293923727384 0.9038654371156385 chr8 146364022 13393514 0.09150823964102325 0.6997143456672981 chr9 141213431 10593222 0.07501568317534896 0.6302612081223655 chr10 135534747 11792126 0.08700444912476946 0.6740955723420138 chr11 135006516 11734382 0.08691715294689925 0.7289757940601966 chr12 133851895 11793573 0.08810912239979868 0.6609555592289006 chr13 115169878 8465259 0.0735023701249384 0.5985940151492379 chr14 107349540 7867270 0.07328648078044862 0.6225468849552879 chr15 102531392 7364995 0.07183161036182947 0.585813627078695 chr16 90354753 7004430 0.07752143376453036 0.6234356834429224 chr17 81195210 6420448 0.0790742212502437 0.6167024623675011 chr18 78077248 6875785 0.08806387489477088 0.7545901942808632 chr19 59128983 4195494 0.07095494945346853 0.7032979969573996 chr20 63025520 5268534 0.08359366174210066 0.6368393970094193 chr21 48129895 3221481 0.066933056886993 0.6011790628397136 chr22 51304566 2544037 0.049586950993796536 0.4576156242314825 chrMT 16571 36798 2.220626395510229 4.294699169925602 chrX 155270560 15540671 0.10008768565013226 0.7706848634282778 chrY 59373566 622393 0.010482661593881695 0.22065478172526104