Number of samples harboring the variant allele (No. samples), mtDNA locus (locus), site-specific nucleotide variability value (Nt Var), amino acid change and variability (AA change and AA Var, respectively), Disease Score, annotations from Mitomap (Lott et al. 2013) and frequencies in 1000 genomes [as implemented in (Calabrese et al. 2014)] are associated with each variant allele.
Sample identifier (sample), heteroplasmic fraction (HF), mtDNA locus (locus), site-specific nucleotide variability (Nt Var), amino acid change and variability (AA change and AA Var, respectively), Disease Score, annotations from Mitomap (Lott et al. 2013) and frequencies in 1000 genomes [as implemented in (Calabrese et al. 2014)] are associated with each variant allele.
Sample identifier (sample), heteroplasmic fraction (HF), mtDNA locus (locus), site-specific nucleotide variability (Nt Var), Amino acid change and variability (AA change and AA Var, respectively), Disease Score, somatic or germline nature ('tumor-specific/germline') of variants and frequencies in 1000 genomes [as implemented in (Calabrese et al. 2014)] are associated with each variant allele.
Thus the RAG complex can act at RSS-like non-antigen receptor locus sites, termed cryptic RSS (cRSS).
The HindIII (Usp22, Emb, Lnp, Mtx2, 19qC2, 3qH2 and 11qA5 loci) or EcoRI (Dlk1 locus) sites investigated are indicated on the maps.
Gene dosage quotients for 9 CDKN2A locus sites and for 15 other 9p genes sites were determined to screen for deletions at 9p.
Within loci, sites had gamma-distributed rates with shape αs chosen uniformly between 0.3 and 1.5.
Unlike the 15-locus NGS subsets used in *BEAST, the 5-locus Sanger dataset was unable to recover the same topology as the 377-locus tree, despite these particular loci having higher average numbers of parsimony informative sites compared to the NGS loci (26%% of Sanger loci sites versus 8%% of NGS loci sites).
