NUMT

NUMT detects and analyzes archaic mitochondrial DNA inserts (NUMTs) in modern human nuclear genomes to identify nuclear integrations of Neanderthal- and Denisovan-like mtDNA and infer ancient interbreeding events.

Key Features:

• Detection of Archaic NUMTs: Identifies archaic NUMTs in high-coverage genomes using next-generation sequencing (NGS) data by targeting reads that map simultaneously to nuclear and mitochondrial DNA.
• flanking_region_analysis.py: Calculates match ratios with archaic genomes for specific genomic regions to aid determination of NUMT origin and integration events.
• numt_stats.py: Computes statistics for discovered NUMTs, including frequency and distribution across genomes and populations.
• mito_variance.py: Calculates pairwise differences between all sequences within an alignment to characterize sequence variation and evolutionary relationships.
• Population scope: Analyzes high-coverage genome data from diverse populations, with emphasis on non‑sub‑Saharan African samples where archaic introgression is more prevalent.

Scientific Applications:

• Inference of archaic introgression: Detects introgressed NUMTs to infer the nature and extent of gene flow from Neanderthals and Denisovans into present-day human genomes.
• Evolutionary and anthropological analysis: Supports tracing lineage, migration patterns, and the genetic contributions of archaic hominins to modern human populations.

Methodology:

Analyzes high-coverage NGS genome data from diverse populations, classifies reads by mtDNA source distinguishing modern versus archaic origins, targets reads mapping to both nuclear and mitochondrial DNA, and applies scripts (flanking_region_analysis.py, numt_stats.py, mito_variance.py) to calculate archaic match ratios, NUMT statistics, and pairwise sequence differences.