BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124945.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 = 4,985,280 number of mapped reads = 4,900,413 (98.3%) number of supplementary alignments = 21,508 (0.43%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,451,661 number of mapped paired reads (second in pair) = 2,448,752 number of mapped paired reads (both in pair) = 4,883,842 number of mapped paired reads (singletons) = 16,571 number of mapped bases = 451,403,645 bp number of sequenced bases = 451,156,823 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 231,531 duplication rate = 2.61% >>>>>>> Insert size mean insert size = 73,176.5293 std insert size = 2,592,645.4389 median insert size = 169 >>>>>>> Mapping quality mean mapping quality = 52.904 >>>>>>> ACTG content number of A's = 130,568,297 bp (28.94%) number of C's = 88,456,954 bp (19.61%) number of T's = 135,951,752 bp (30.13%) number of G's = 95,886,141 bp (21.25%) number of N's = 293,679 bp (0.07%) GC percentage = 40.86% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 3,827,870 number of insertions = 67,800 mapped reads with insertion percentage = 1.35% number of deletions = 149,278 mapped reads with deletion percentage = 2.99% homopolymer indels = 47.23% >>>>>>> Coverage mean coverageData = 0.1458X std coverageData = 1.417X There is a 9.95% of reference with a coverageData >= 1X There is a 2.99% of reference with a coverageData >= 2X There is a 0.71% of reference with a coverageData >= 3X There is a 0.22% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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% 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 34414365 0.13807133102388539 1.4459716571319052 chr2 243199373 36295860 0.1492432301624396 1.6116710156923721 chr3 198022430 44155020 0.222979891722367 0.6325848631952433 chr4 191154276 26445960 0.13834877541530904 0.7806033093775423 chr5 180915260 23411768 0.12940737005822506 0.4692676501103805 chr6 171115067 22119495 0.12926678747699055 0.9740829110532152 chr7 159138663 30918558 0.19428690311417282 2.7868654452978463 chr8 146364022 28554580 0.1950928896993552 0.7744848417043565 chr9 141213431 18261185 0.12931620505701047 1.7670724605894457 chr10 135534747 22500648 0.16601387096697795 3.1941700222648977 chr11 135006516 20573413 0.15238829657673708 1.1423914331537635 chr12 133851895 24436405 0.18256301115497842 0.5563775612620039 chr13 115169878 9633319 0.08364443174976707 0.3646172488056549 chr14 107349540 13022297 0.12130743177846873 0.4882258683091684 chr15 102531392 11764514 0.1147406054918283 0.4365212693848615 chr16 90354753 14858038 0.16444113349521303 2.5519231157461224 chr17 81195210 10407575 0.12817966724884386 1.40889578888978 chr18 78077248 12048527 0.1543154671640066 1.7960921608283715 chr19 59128983 5722991 0.09678825357101102 0.8469603304289951 chr20 63025520 13568114 0.2152796835313695 0.6370574143107632 chr21 48129895 5492454 0.11411730692535274 0.5619600056045917 chr22 51304566 4425694 0.08626316028089975 0.3922941129941366 chrMT 16571 86408 5.214410717518557 3.6567186838679655 chrX 155270560 14190508 0.09139213512207336 0.6148160824616922 chrY 59373566 4095949 0.06898607033305024 1.1822853949435135