meth_table.tab

Methylation counts: each row (953,489 total) is a genomic position (*seqnames* + *start*) in a subject (*sample*).
Positions according T2T-CHM13v2.0 annotation. Methylation call with Nanopore (model sup V5.0.0 5mCG_5hmCG), in table only 5mC.

Data already filtered: 13 genes (see metadata section), 100 subject with highest coverage out of 158, only sites with cov >= 10 in 90 samples.
3,856 unique positions in 100 subjects.

Columns:

- seqnames: chromosome name
- start: CpG position (mapped on T2T-CHM13v2.0 reference)
- Nvalid_cov: Number of calls passing filters were classified as the canonical base rather than modified
- perc_modified: (Nmod / Nvalid_cov) * 100
- Nmod: Number of calls passing filters that were classified as 5mC
- sample: sample id
- gene_id: gene name
- element: single value, follows the order CDS > exon > intron > else
- CpG: binary, 1 the position includes a CpG island
- any_repeat: binary, 1 if the position includes any TE
- te_type: single value, if more than one TE in the same position, LINE > SINE > LTR > DNA
- core15_e30: chromatin state (15 states) in the position according roadmap epigenomics sample E30
- rep_name: specific name of the TE
- rep_class: broad taxonomical classification of the TE
- rep_id: number classifying an individual TE, values from the repeatmasker file from the reference T2T-CHM13v2.0