Additional file 1 of The association of visceral adiposity index with the risk of kidney stone and kidney stone recurrence

Additional file 1: Supplemental Table 1. Multivariate logistic regression models of kidney stones

python_scripts

Custom python_scripts used in the analysis, including mutual best hit analysis, pairwise_p_distance calculator, gene_average_bootstrap_value calculator, parse_gene_tree_topology. All scripts call module of Biopython. Please install Biopython before use

Supplementary File Archives

These are supplementary tables and figures related to the paper

data_nex_new

These data sets were generated from genomic and transcriptomic data of jawed vertebrate. The compressed file contains data sets generated by different filtering approach,including data filtered by data completeness,alignment quality, gene informative, evolutionary rate,resolution of gene and specific data sets designed for neoaves,eutheria,teleostei questions

Phylogram derived from analysis of the concatenated four long NPCL markers.

<p>Phylogenetic relationships among osteichthyans were based on maximum likelihood and Bayesian inference analyses of the combined data set (7,134 bp) under 3-partition and 4-partition strategies (by codon and by gene). The two quarter circles above the branches represent the bootstrap proportions for partitioned ML analyses and the two quarter circles below branches represent the Bayesian posterior probabilities for partitioned BI analyses. Branch lengths were estimated in the 4-partition ML (by gene) analysis on a concatenated dataset (4 GTR +Γ+I models for 4 gene partitions).</p

Comparison amplification efficiency between nested PCR and standard PCR for three long NPCL markers.

<p>Each long NPCL marker was amplified in two contiguous and overlapping fragments (F1 and F2). Three different color cells are used to represent the agarose gel electrophoretic images of PCR products. For complete species names, please refer to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039256#pone.0039256.s006" target="_blank">Table S1</a>.</p

Phylogenetic informativeness (PI) profile of the reference NPCL marker RAG1 and three long NPCL markers.

<p>The timetree was newly estimated based on the concatenated dataset (7,134 bp). The PI profile was generated using the online program PhyDesign <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039256#pone.0039256-LopezGiraldez1" target="_blank">[52]</a>. For more detail, please see the text.</p

PCR primers used to amplify three long NPCL markers together with the reference marker RAG1.

<p>R = A+G; Y = C+T; W = A+T; M = A+C; K = G+T; D = A+T+G; H = A+C+T; N = A+G+C+T.</p><p>Each long NPCL marker is amplified in two contiguous and overlapping fragments (F1 and F2). * indicates NPCL marker that is amplified using both nested PCR and standard PCR in order to compare amplification difficulties between two PCR methods. For nested PCR, 1st PCR and 2nd PCR represent two separate runs, products of 1st PCR (no dilution) are used as amplification templates in 2nd PCR; For standard PCR, primers in 2nd PCR are used alone to amplify target fragments.</p

Characteristical information of the 4 NPCL markers.

<p>Length, length of refined alignment; Alpha, shape parameter of the gamma distribution; Pinvar, proportion of invariable sites; Sub. Rate, relative substitution rate estimated by MrBayes; Treeness, proportion of tree distance on internal branches; RCV, relative composition variability.</p

tree_nex

These are trees generated from different data sets.Names were refered as corresponding data set