BatMeth2 Report
Summary
General
batmeth2 version:2.1 (https://github.com/GuoLiangLi-HZAU/BatMeth2)
ProgramBatMeth2.v1
Workdir/public/home/scheng/ASM/Arabidopsis/batmeth2-mbw-new
outputdir./
AlignerBatMeth2-align
Genome../arad_genome/batmeth2-index/TAIR10_allChr.fa
Annotation../arad_genome/TAIR10.gene.gff/None
Output-prefixBS-cviler
Input../rawdata/BS-cviler-TCCACGATT_TKD180401385-AK7028_1.fq.gz || ../rawdata/BS-cviler-TCCACGATT_TKD180401385-AK7028_2.fq.gz
Alignment-ModePaired-end
Paramaters
Threads8
Calmeth----
Quality_Score30
redup1
meth region length1000
Print methstate samfile0
calmeth and bmtools----
Coverage4
maxCoverage1000
binCoverage1
chromStep50000
bmtools----
Gene bins step0.010
Distance of upstream and downstream2000
Alignment
Total_reads17849870
Total_Mapped_Q3016602117
Mapped_forword8301131
Mapped_reverse8300986
DNA Methylation level
CaseValue
Raw count of Met_C in CG:7966418
Raw count of Non_Met_C in CG:19958344
Raw count of Met_C in CHG:3755751
Raw count of Non_Met_C in CHG:25197763
Raw count of Met_C in CHH:4955766
Raw count of Non_Met_C in CHH:90991084
[CpG]M: 426730 Mh: 152678 H: 120264 hU: 103129 U: 1458251
[mC]M: 553005 Mh: 344552 H: 454967 hU: 760685 U: 10788994
##2155143921528650
Strand+
mC/(C+T){8326495 / 76153938} = 10.933768%
mCG/(CG+TG){3978853 / 13938711} = 28.545344%
mCHG/(CHG+THG){1879193 / 14421962} = 13.030079%
mCHH/(CHH+THH){2468449 / 47793265} = 5.164847%
Strand-
mC/(C+T){8351440 / 76671188} = 10.892540%
mCG/(CG+TG){3987565 / 13986047} = 28.511022%
mCHG/(CHG+THG){1876558 / 14531552} = 12.913679%
mCHH/(CHH+THH){2487317 / 48153589} = 5.165382%
Strand+-
mC/(C+T){16677935 / 152825126} = 10.913084%
mCG/(CG+TG){7966418 / 27924758} = 28.528154%
mCHG/(CHG+THG){3755751 / 28953514} = 12.971659%
mCHH/(CHH+THH){4955766 / 95946854} = 5.165116%
DNA methylation level
DNA methylation level in chromosome
DNA methylation Coverage
DNA methylation distribution
Heatmap of DNA methylation in function elements
Enrichment of DNA methylation