BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124862.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 3,780,112 number of mapped reads = 3,751,576 (99.25%) number of supplementary alignments = 53,512 (1.42%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,880,248 number of mapped paired reads (second in pair) = 1,871,328 number of mapped paired reads (both in pair) = 3,739,752 number of mapped paired reads (singletons) = 11,824 number of mapped bases = 534,022,648 bp number of sequenced bases = 533,626,937 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 510,358 duplication rate = 11.39% >>>>>>> Insert size mean insert size = 61,672.6219 std insert size = 2,330,262.7251 median insert size = 181 >>>>>>> Mapping quality mean mapping quality = 53.6609 >>>>>>> ACTG content number of A's = 157,822,572 bp (29.58%) number of C's = 107,353,213 bp (20.12%) number of T's = 157,288,782 bp (29.48%) number of G's = 111,129,838 bp (20.83%) number of N's = 32,532 bp (0.01%) GC percentage = 40.94% >>>>>>> Mismatches and indels general error rate = 0.0117 number of mismatches = 5,966,709 number of insertions = 99,987 mapped reads with insertion percentage = 2.54% number of deletions = 214,685 mapped reads with deletion percentage = 5.51% homopolymer indels = 48.54% >>>>>>> Coverage mean coverageData = 0.1725X std coverageData = 2.1682X There is a 9.34% of reference with a coverageData >= 1X There is a 5.08% of reference with a coverageData >= 2X There is a 1.11% of reference with a coverageData >= 3X There is a 0.51% of reference with a coverageData >= 4X There is a 0.16% of reference with a coverageData >= 5X There is a 0.08% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% 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 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% 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 45298788 0.1817399203189949 3.0316351498081984 chr2 243199373 47757326 0.19637109015079574 2.150847680063232 chr3 198022430 32035890 0.16177909744870822 0.6126669493605577 chr4 191154276 39338661 0.20579534930204751 1.810861905761283 chr5 180915260 35887696 0.19836743456577405 0.6399581944355491 chr6 171115067 28068952 0.16403553756023131 1.961388854578081 chr7 159138663 22362938 0.14052485787190508 0.8271883768798249 chr8 146364022 25776246 0.17611053350255707 0.838536099627011 chr9 141213431 27994261 0.19824078206838555 3.640573942513744 chr10 135534747 22015439 0.16243391076680874 4.62619188190788 chr11 135006516 27456816 0.20337400603686417 2.458783707133387 chr12 133851895 25514177 0.19061498531642007 0.6340182540976124 chr13 115169878 9233933 0.08017663264347645 0.38889377627403693 chr14 107349540 17139100 0.15965694869302655 0.5986581210738401 chr15 102531392 23755367 0.23168872027017834 0.7122458833531862 chr16 90354753 21484879 0.23778360613746574 3.2459014615070867 chr17 81195210 9854851 0.12137231986960807 4.140716627474649 chr18 78077248 9204222 0.11788609660012607 2.960410544126475 chr19 59128983 6658324 0.1126067735682178 1.64349097446018 chr20 63025520 8235667 0.13067194050917788 0.854783867217326 chr21 48129895 7146783 0.14848947831695872 1.1621453364870646 chr22 51304566 5112636 0.09965265079915109 0.45453107838626045 chrMT 16571 37984 2.292197211996862 2.0868442664230225 chrX 155270560 35252583 0.22703971055427377 1.1953032150823983 chrY 59373566 1399129 0.0235648470230001 1.8548904204151049