Additional file 5: Figure S4. of Recombination in pe/ppe genes contributes to genetic variation in Mycobacterium tuberculosis lineages
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posted on 2016-02-29, 05:00 authored by Jody Phelan, Francesc Coll, Indra Bergval, Richard Anthony, Rob Warren, Samantha Sampson, Nicolaas Gey van Pittius, Judith Glynn, Amelia Crampin, Adriana Alves, Theolis Bessa, Susana Campino, Keertan Dheda, Louis Grandjean, Rumina Hasan, Zahra Hasan, Anabela Miranda, David Moore, Stefan Panaiotov, Joao Perdigao, Isabel Portugal, Patricia Sheen, Erivelton de Oliveira Sousa, Elizabeth Streicher, Paul van Helden, Miguel Viveiros, Martin Hibberd, Arnab Pain, Ruth McNerney, Taane ClarkIdentifying sites leading to differences in tree topologies based on all SNPs (Additional file 4: Figure S3a) and only those from pe/ppe genes (Additional file 4: Figure S3b). The Î Site wise log likelihood score (Î SSLS) is calculated for each SNP in the pe/ppe gene alignments. Negative differences indicate SNP positions favouring the pe/ppe tree. SNPs in pe_pgrs3, ppe57 and ppe60 produce strong phylogenetic signals supporting the pe/ppe tree. (TIF 113Â kb)
