batmeth2 version: | 2.1 (https://github.com/GuoLiangLi-HZAU/BatMeth2) |
Program | BatMeth2.v1 |
Workdir | /public/home/ppguan/qwzhou/arabidopsis_shzky/BS-Seq/TEST |
outputdir | ./ |
Aligner | BatMeth2-align |
Genome | /public/home/ppguan/qwzhou/arabidopsis_shzky/TAIR10/batmeth2index/TAIR10_allChr.fa |
Annotation | /public/home/ppguan/qwzhou/arabidopsis_shzky/TAIR10/TAIR10.gene.gff/None |
Output-prefix | Col0 |
Input | RL303JKZ0341_1406BSDNA20190725_S20190729_R1.fq.gz || RL303JKZ0341_1406BSDNA20190725_S20190729_R2.fq.gz |
Alignment-Mode | Paired-end |
Threads | 12 |
Calmeth | ---- |
Quality_Score | 10 |
redup | 1 |
meth region length | 1000 |
Print methstate samfile | 1 |
calmeth and methyGff | ---- |
Coverage | 5 |
maxCoverage | 1000 |
binCoverage | 3 |
chromStep | 50000 |
methyGff | ---- |
Gene bins step | 0.025 |
Distance of upstream and downstream | 2000 |
in total (QC-passed reads + QC-failed reads) | 66866129 + 0 |
secondary | 0 + 0 |
supplementary | 0 + 0 |
duplicates | 0 + 0 |
mapped (100.00% : N/A) | 66866119 + 0 |
paired in sequencing | 66866129 + 0 |
read1 | 33447473 + 0 |
read2 | 33418656 + 0 |
properly paired (98.68% : N/A) | 65980814 + 0 |
with itself and mate mapped | 66760577 + 0 |
singletons (0.16% : N/A) | 105542 + 0 |
with mate mapped to a different chr | 779763 + 0 |
with mate mapped to a different chr (mapQ>=5) | 751693 + 0 |
Case | Value |
Raw count of Met_C in CG: | 43756947 |
Raw count of Non_Met_C in CG: | 137165865 |
Raw count of Met_C in CHG: | 14130450 |
Raw count of Non_Met_C in CHG: | 166354090 |
Raw count of Met_C in CHH: | 18785881 |
Raw count of Non_Met_C in CHH: | 878347105 |
[CpG] | M: 1227386 Mh: 343320 H: 113820 hU: 98428 U: 3707711 |
[mC] | M: 1369039 Mh: 651959 H: 644200 hU: 1116781 U: 38226104 |
Strand | + |
mC/(C+T) | {24999591 / 410770214} = 6.086028% |
mCG/(CG+TG) | {14180709 / 55772723} = 25.425886% |
mCHG/(CHG+THG) | {4859264 / 60654505} = 8.011382% |
mCHH/(CHH+THH) | {5959618 / 294342986} = 2.024719% |
Strand | - |
mC/(C+T) | {51520926 / 845933631} = 6.090422% |
mCG/(CG+TG) | {29511744 / 124977029} = 23.613735% |
mCHG/(CHG+THG) | {9242781 / 119652335} = 7.724698% |
mCHH/(CHH+THH) | {12766401 / 601304267} = 2.123118% |
Strand | +- |
mC/(C+T) | {76520517 / 1256703845} = 6.088986% |
mCG/(CG+TG) | {43692453 / 180749752} = 24.172898% |
mCHG/(CHG+THG) | {14102045 / 180306840} = 7.821137% |
mCHH/(CHH+THH) | {18726019 / 895647253} = 2.090781% |