Metadata.

Metadata table for the LA and CU sequences used in this study (tab-separated format). It contains the following columns: id—identifier of the sequence used in these analyses (corresponds to the tree tips);POL Accession Number—GenBank [40] accession number for the pol part of the sequence;ENV Accession Number—GenBank accession number for the env part of the sequence;source—source of the data: LA or CU;province_of_diagnostics—province of diagnostics for CU sequences, abroad for LA;country_code—ISO2 code for the country of sampling;country—country of sampling;intregion—generalized location of sampling, includes the following values: Australia, Cuba, Eastern Africa, Eastern Asia, Middle Africa, Northern America, Northern Europe, Russia, South America, Southern Africa, Southern Asia, Southern Europe, Western Africa, Western Asia, Western Europe;subregion—generalized location of sampling, includes the following values: Asia, Australia and New Zealand, Cuba, Europe, Northern America, Russia, South America, Sub-Saharan Africa;region—generalized location of sampling, includes the following values: Africa, Americas, Asia, Cuba, Europe, Oceania;sample_date—date of sampling;diagnostics_date—date of diagnostics;gender—gender of the infected individual: F or M;risk_group—declared risk group: Bisexual, HT (heterosexual), or MSM (men-who-have-sex-with-men);treated—treatment status: naive or treated;subtype_annotated—pre-annotated HIV-1 subtype;subtype_jpHMM—HIV-1 subtype detected by jpHMM;subtype_consensus—HIV-1 subtype annotations used in this study: pre-annotated ones when compatible with jpHMM (e.g. matching jpHMM breakpoints for CRF19), otherwise jpHMM prediction;subtype_tree—HIV-1 subtype detected by the phylogenetic trees in this study (same as consensus for the majority of the sequences, see Phylogenetic trees);subtype_CRF_19_D—whether the sequence is compatible with CRF19 in its D part according to jpHMM: D if yes, empty otherwise;subtype_CRF_19_G—whether the sequence is compatible with CRF19 in its G part according to jpHMM: G if yes, empty otherwise;subtype_CRF_19_A1—whether the sequence is compatible with CRF19 in its A1 part according to jpHMM: A1 if yes, empty otherwise. id—identifier of the sequence used in these analyses (corresponds to the tree tips); POL Accession Number—GenBank [40] accession number for the pol part of the sequence; ENV Accession Number—GenBank accession number for the env part of the sequence; source—source of the data: LA or CU; province_of_diagnostics—province of diagnostics for CU sequences, abroad for LA; country_code—ISO2 code for the country of sampling; country—country of sampling; intregion—generalized location of sampling, includes the following values: Australia, Cuba, Eastern Africa, Eastern Asia, Middle Africa, Northern America, Northern Europe, Russia, South America, Southern Africa, Southern Asia, Southern Europe, Western Africa, Western Asia, Western Europe; subregion—generalized location of sampling, includes the following values: Asia, Australia and New Zealand, Cuba, Europe, Northern America, Russia, South America, Sub-Saharan Africa; region—generalized location of sampling, includes the following values: Africa, Americas, Asia, Cuba, Europe, Oceania; sample_date—date of sampling; diagnostics_date—date of diagnostics; gender—gender of the infected individual: F or M; risk_group—declared risk group: Bisexual, HT (heterosexual), or MSM (men-who-have-sex-with-men); treated—treatment status: naive or treated; subtype_annotated—pre-annotated HIV-1 subtype; subtype_jpHMM—HIV-1 subtype detected by jpHMM; subtype_consensus—HIV-1 subtype annotations used in this study: pre-annotated ones when compatible with jpHMM (e.g. matching jpHMM breakpoints for CRF19), otherwise jpHMM prediction; subtype_tree—HIV-1 subtype detected by the phylogenetic trees in this study (same as consensus for the majority of the sequences, see Phylogenetic trees); subtype_CRF_19_D—whether the sequence is compatible with CRF19 in its D part according to jpHMM: D if yes, empty otherwise; subtype_CRF_19_G—whether the sequence is compatible with CRF19 in its G part according to jpHMM: G if yes, empty otherwise; subtype_CRF_19_A1—whether the sequence is compatible with CRF19 in its A1 part according to jpHMM: A1 if yes, empty otherwise. (TAB)