| 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% |