BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124961.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 = 6,023,576 number of mapped reads = 5,895,276 (97.87%) number of supplementary alignments = 58,937 (0.98%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,954,393 number of mapped paired reads (second in pair) = 2,940,883 number of mapped paired reads (both in pair) = 5,865,616 number of mapped paired reads (singletons) = 29,660 number of mapped bases = 500,363,963 bp number of sequenced bases = 500,053,621 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 820,514 duplication rate = 9.53% >>>>>>> Insert size mean insert size = 83,450.3127 std insert size = 2,719,350.4035 median insert size = 164 >>>>>>> Mapping quality mean mapping quality = 52.3386 >>>>>>> ACTG content number of A's = 144,379,065 bp (28.87%) number of C's = 91,303,960 bp (18.26%) number of T's = 151,600,297 bp (30.32%) number of G's = 112,764,999 bp (22.55%) number of N's = 5,300 bp (0%) GC percentage = 40.81% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 3,894,798 number of insertions = 81,801 mapped reads with insertion percentage = 1.34% number of deletions = 163,746 mapped reads with deletion percentage = 2.72% homopolymer indels = 45.76% >>>>>>> Coverage mean coverageData = 0.1616X std coverageData = 2.491X There is a 10.07% of reference with a coverageData >= 1X There is a 3.23% of reference with a coverageData >= 2X There is a 0.99% of reference with a coverageData >= 3X There is a 0.42% of reference with a coverageData >= 4X There is a 0.18% of reference with a coverageData >= 5X There is a 0.09% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% 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 0.01% 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 39835082 0.15981938917616578 1.4280474908119143 chr2 243199373 49916116 0.2052477166542695 2.534514704760154 chr3 198022430 38446247 0.1941509706753927 0.741051483651701 chr4 191154276 33490930 0.17520366638306328 2.0310027376088424 chr5 180915260 25394176 0.14036503056734959 0.5555804132650006 chr6 171115067 27792628 0.1624206943740378 0.7732990863229059 chr7 159138663 28188981 0.1771347105008668 1.1913015421422868 chr8 146364022 29351870 0.20054019832824763 0.8147537343670257 chr9 141213431 21224523 0.15030102200406137 1.819590053777081 chr10 135534747 29491074 0.21759050466962543 9.176797531877126 chr11 135006516 19526498 0.1446337449371703 0.8633491529105344 chr12 133851895 17652990 0.13188449816119524 0.5120750413139834 chr13 115169878 15541542 0.13494450345775308 0.5247878653443211 chr14 107349540 12841996 0.11962786240164607 0.5964604560079135 chr15 102531392 12429038 0.12122178152033672 0.5119223909338947 chr16 90354753 18932342 0.2095334376045497 3.840551884514959 chr17 81195210 9784948 0.1205113946992686 1.5400771507316497 chr18 78077248 10924092 0.1399138965553704 1.8638173364552166 chr19 59128983 6904178 0.11676470065449968 0.8878939775882042 chr20 63025520 10888352 0.17276100220989846 0.8009986531472452 chr21 48129895 5239901 0.1088699861073871 1.0288362869420367 chr22 51304566 4084074 0.07960449368190738 0.4911992431734716 chrMT 16571 3258741 196.65324965300826 114.65779568248395 chrX 155270560 20750600 0.13364156089860177 0.6891130523901233 chrY 59373566 8473044 0.14270734555509096 3.589953424453176