Table 2.
Mutation list column description in alphabetical order.
| Column name | Column description | Possible values |
|---|---|---|
| alg | algorithm used for detection of mutations | e.g.,: mutect2, somatic sniper |
| alt | alternative allele | e.g.,: G, A, GAA |
| arm | in which part of miRNA precursor mutation is located | 5p, loop, 3p |
| balance | arm from which the main miRNA is generated; defined based on deep sequencing reads (miRBase), [for details see Urbanek-Trzeciak et al. (2020)] | 5p, 3p, both, undefined |
| based_on_coordinates | indicates whether used coordinates were defined based on miRBase annotations or were predicted based on miRNA structure | yes, no |
| chrom | chromosome | e.g.,: chr1, chrX |
| confidence | as high-confidence miRNA genes, we considered genes coding for miRNA precursors annotated as “high confidence” in miRBase and/or deposited in MirGeneDB v2.0 | High, Low |
| cut_region | whether the mutation is within Drosha or Dicer cut region | 0 (no), 1 (yes) |
| duplex | whether the mutation is within duplex | 0 (no), 1 (yes) |
| from_start | nucleotide position from start of miRNA region in which mutation is located (e.g., within the seed, 5′ flanking sequence) | e.g.,: 1, 3 |
| from_end | nucleotide position from end of miRNA region in which mutation is located (e.g., within the seed, 5′ flanking sequence) | e.g.,: -1, -25 |
| hgvs | noncoding HGVS nomenclature of the mutation in the reference to the miRBase coordinates ∗Note that annotation of some indels may not match the latest HGVS recommendations; for multimutations (multiple changes in a single position in one sample) HGVS nomenclature is not available |
e.g.,: n.90G>A, n.67+21G>A, n.1–15delA |
| hgvs_g | genomic HGVS nomenclature of the mutation; for multimutations HGVS is not available | e.g.,: NC_000010.11:g.17845137C>A, NC_000001.11:g.1167872_1167873insT |
| ID | miRBase ID | e.g.,: MI0000737 |
| indiv_name | sample identifier | e.g.,: sample01 |
| mirgenedb_ID | mirGeneDB ID | e.g.,: Hsa-Mir-8-P1a_pre |
| motifs | whether any motif was disturbed as a result of the mutation | 0 (no), 1 (yes) |
| motifs_{} | information for each checked motif if there was the loss of a motif as a result of the mutation | -, loss |
| mutation_type | mutation type: substitution, insertion, deletion, insertion-deletion, multimutation | subst, ins, del, indel, multimutation |
| name | miRNA region name built by pre-miRNA name and precursor region connected by an underscore | e.g.,: hsa-mir-200a_flanking-5, hsa-mir-511_post-seed |
| no_of_loc | internal check column | 1 |
| orientation | miRNA gene orientation | +, - |
| pos | genomic position of the mutation | e.g.,: 1167859, 20633667 |
| pre_name | precursor name | e.g.,: hsa-mir-200a, hsa-mir-6084 |
| ref | reference allele | e.g.,: C, GCA |
| seed | whether mutation is located within seed | 0 (no), 1 (yes) |
| start | miRNA region start coordinate | e.g.,: 1167853, 20633667 |
| start_pre_build | miRBase start coordinate | e.g.,: 1167863, 20633679 |
| stop | miRNA region stop coordinate | e.g.,: 1167877, 20633691 |
| stop_pre_build | miRBase stop coordinate | e.g.,: 1167952, 20633788 |
| type | region of miRNA precursor | flanking-5, pre-seed, seed, post-seed, loop, flanking-3 |
| type_of_subst | substitution type, n.a. for non-substitution mutations | transition, transversion, n.a. |
| weight | weight score | 1, 1.5, 2 |
A description of all the columns present in transitional or summary files is included in Table S1.