BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124818.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 = 27,441,724 number of mapped reads = 27,089,249 (98.72%) number of supplementary alignments = 123,304 (0.45%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 13,551,762 number of mapped paired reads (second in pair) = 13,537,487 number of mapped paired reads (both in pair) = 27,000,338 number of mapped paired reads (singletons) = 88,911 number of mapped bases = 2,481,670,109 bp number of sequenced bases = 2,479,717,882 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,375,526 duplication rate = 4.88% >>>>>>> Insert size mean insert size = 64,967.5702 std insert size = 2,421,502.3156 median insert size = 169 >>>>>>> Mapping quality mean mapping quality = 52.9016 >>>>>>> ACTG content number of A's = 709,655,166 bp (28.62%) number of C's = 491,085,899 bp (19.8%) number of T's = 732,410,388 bp (29.54%) number of G's = 546,548,090 bp (22.04%) number of N's = 18,339 bp (0%) GC percentage = 41.84% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 18,389,910 number of insertions = 400,490 mapped reads with insertion percentage = 1.44% number of deletions = 1,039,725 mapped reads with deletion percentage = 3.75% homopolymer indels = 47.03% >>>>>>> Coverage mean coverageData = 0.8017X std coverageData = 7.0166X There is a 30.74% of reference with a coverageData >= 1X There is a 17.9% of reference with a coverageData >= 2X There is a 10.43% of reference with a coverageData >= 3X There is a 6.37% of reference with a coverageData >= 4X There is a 3.97% of reference with a coverageData >= 5X There is a 2.53% of reference with a coverageData >= 6X There is a 1.64% of reference with a coverageData >= 7X There is a 1.08% of reference with a coverageData >= 8X There is a 0.72% of reference with a coverageData >= 9X There is a 0.49% of reference with a coverageData >= 10X There is a 0.34% of reference with a coverageData >= 11X There is a 0.24% of reference with a coverageData >= 12X There is a 0.17% of reference with a coverageData >= 13X There is a 0.12% of reference with a coverageData >= 14X There is a 0.09% of reference with a coverageData >= 15X There is a 0.07% of reference with a coverageData >= 16X There is a 0.06% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% 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 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 190523257 0.7643842821157906 7.14460834387023 chr2 243199373 205866548 0.8464929224961447 9.36033258117956 chr3 198022430 180195096 0.9099731580912324 2.148765414542161 chr4 191154276 132621496 0.6937929863520291 3.986355756669594 chr5 180915260 129781372 0.7173600060050214 1.723089313164804 chr6 171115067 129899466 0.7591351730587231 4.64355196513045 chr7 159138663 169623553 1.0658852462521946 8.376686875696914 chr8 146364022 160080219 1.093712900291849 3.468256983328485 chr9 141213431 93570028 0.6626142239968661 8.502110253157747 chr10 135534747 119523434 0.8818656222525726 19.292633511106033 chr11 135006516 159936602 1.184658390858705 9.392617560588029 chr12 133851895 127064835 0.9492942554156593 1.961738073688473 chr13 115169878 63493273 0.5513010355016613 1.3653272060924906 chr14 107349540 70024903 0.6523074342004632 1.9173539383525804 chr15 102531392 65463008 0.6384679533074125 1.5149103532994748 chr16 90354753 75018213 0.8302630521274293 8.996753576436697 chr17 81195210 65857385 0.8110993862815307 6.673827507456465 chr18 78077248 57867718 0.7411598062472694 8.57164251611787 chr19 59128983 37715911 0.6378582733276505 3.8183561618094535 chr20 63025520 74513102 1.1822687381238584 2.4489551754067587 chr21 48129895 15629126 0.32472803026061037 2.0456802435837256 chr22 51304566 27940048 0.5445918400323277 1.7275389729642505 chrMT 16571 1256685 75.83640094140365 43.293290649390336 chrX 155270560 121936351 0.7853153295769655 3.8117335918964246 chrY 59373566 6268480 0.10557694985003932 6.595916008155008