Data · dataset · 2026
RAD-seq SNP data for estimating genetic uniqueness
Listed in ScienceDB
RAD-seq SNP datasets of two frog species, Leptobrachium boringii and Quasipaa boulengeri.
Description
The full SNP dataset of L. boringii contained 17,686 loci, and the Q. boulengeri full SNP dataset comprised 37,493 loci. These loci showed unique BLAST hits from throughout the genomes of congeners.
For each species, the commonly used minor allele frequency (MAF) filters of different strengths, 1%, 2%, 5%, and 10%, were applied to the full SNP dataset. Then, according to the BLAST hit locations, the first locus from a chromosome and every first locus after 10, 50, or 300 kb were retained to reflect different extents of thinning for reducing the effects of linkage disequilibrium. One SNP was randomly selected from each retained locus.
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It was performed with 10 replicates to account for uncertainty. A total of 300 SNP datasets with a genotype depth ≥6 and 40 datasets with depths ≥10 from the two species were generated to quantify genetic uniqueness. 6x: genotype read depth ≥6; 10x: genotype read depth ≥10; maf01: minimum MAF 1%; maf02: minimum MAF 2%; maf05: minimum MAF 5%; maf10: minimum MAF 10%; 10kb: physical distance of at least 10kb assumed; 50kb: physical distance of at least 50kb assumed; 300kb: physical distance of at least 300kb assumed.
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Where it is published
- DOI doi.org/10.57760/sciencedb.16715 ↗
DOI / persistent id · from scidb cn
Catalogue records · 1
- OAI-PMH record scidb.cn/oai?verb=GetRecord&metadataPrefix=oai_dc&identifier=10.57760%2… ↗
metadata API · from scidb cn
Topics
- From keywords
- Earth & Environmental Science · Engineering · Humanities · Life Sciences · Social Science
- Inferred from text
- Evolutionary biology 68%
Provenance · 1 source records, 11 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| ScienceDB | 10.57760/sciencedb.16715 | 12 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| access_level | source · scidb cn | connector:scidb_cn@1.0.0 | |
| concepts[field].anzsrc:group:3104 | enrichment · scidb cn | taxonomy-embedding@1.0.0 | title+keywords+description (68%) |
| concepts[field].local:field:earth-environmental | mapping · scidb cn | connector:scidb_cn@1.0.0 | |
| concepts[field].local:field:engineering | mapping · scidb cn | connector:scidb_cn@1.0.0 | |
| concepts[field].local:field:humanities | mapping · scidb cn | connector:scidb_cn@1.0.0 | |
| concepts[field].local:field:life-sciences | mapping · scidb cn | connector:scidb_cn@1.0.0 | |
| concepts[field].local:field:social-science | mapping · scidb cn | connector:scidb_cn@1.0.0 | |
| description | source · scidb cn | connector:scidb_cn@1.0.0 | /metadata/dc/description |
| license | source · scidb cn | connector:scidb_cn@1.0.0 | /metadata/dc/rights |
| publication_date | source · scidb cn | connector:scidb_cn@1.0.0 | |
| title | source · scidb cn | connector:scidb_cn@1.0.0 | /metadata/dc/title |