Additional file 4.
Multi-alignments of sequenced NumtS from 4 different phylo-geographic samples. The nucleotide multi-alignments of the amplified (fig 2a in the manuscript) and sequenced NumtS 87, 122 and 41–54 of individuals coming from Europe, Japan, Latin America and North Africa belonging respectively to haplogroups H2b, G1a1a, I3a and L2a1c1 compared with the NumtS sequence as it can be extracted from the Human Genome build36.2 through the UCSC genome browser (hg18 release) and the sequences of the corresponding mitochondrial region for the same samples, are reported. Multi-alignments of NumtS 87 and 122 include the rCRS sequence (accession number J01415.2 in GenBank) also, thus allowing the exact localization of the variant sites respect to the universally used human mitochondrial reference sequence. As far as NumtS 41-54 the reference sequence has been added to NumtS 43 only in a distinctly reported multialignment. The conservation of NumtS is evident from the multialignment among the different subjects, although heterozygous sites can be observed (nucleotide ambiguity letter such as Y for C/T, R for A/G etc.). Each multi-alignment refers to the nuclear region (from Chromosome start to Chromosome end), as reported in additional file 1. The NumtS sequences produced in our validation experiments are named with a code defined by the NumtS code and the haplogroup of the sample. The corresponding mtDNA regions are coded as mt, followed by the haplogroup code. The reference sequence for 122 NumtS is extracted from Celera genome chromosome 9 (CM00260). Sequencing of L2a1c1 122 NumtS, H2b and L2a1c1 41, 42 and 54 NumtS failed.
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Lascaro et al. BMC Genomics 2008 9:267 doi:10.1186/1471-2164-9-267