EMPOP SAM2
Definition
The submission quality-assurance module used by the EMPOP database to screen incoming mtDNA sequences for phylogenetic inconsistencies, sequencing artefacts, and nomenclature errors. Only sequences passing SAM2 are included in the frequency-estimation dataset.
- Function
- Submission quality-assurance module
- Checks
- Phylogenetic inconsistencies, artefacts, nomenclature
- Role
- Gatekeeper before frequency dataset inclusion
Common questions
What happens to a sequence that fails SAM2?+
It is excluded from the frequency-estimation dataset until the submitting laboratory corrects the flagged inconsistency or artefact, or it may be rejected from the database entirely.
Why does nomenclature matter for mtDNA submissions?+
mtDNA variants are named relative to the rCRS reference sequence, and inconsistent notation could let the same variant be counted more than once or different variants be conflated, skewing the population frequency estimate.
Related terms
- E-Value (BLAST)
- The expected number of alignments as good as the query result that would occur by chance in a database of the given...
- Haplogroup
- A monophyletic branch of the human mitochondrial (or Y-chromosome) phylogenetic tree defined by a set of derived mutations. Haplogroup assignment is the...
- INSDC
- International Nucleotide Sequence Database Collaboration, the three-way partnership between GenBank (NCBI/NLM, US), ENA (EMBL-EBI, UK/EU), and DDBJ (National Institute of Genetics, Japan)...
- rCRS
- The revised Cambridge Reference Sequence (GenBank accession NC_012920), the standard reference for human mitochondrial DNA. All mtDNA variant positions in forensic and...