Computational protocol: Genetic Variation of 25 Y-Chromosomal and 15 Autosomal STR Loci in the Han Chinese Population of Liaoning Province, Northeast China

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Protocol publication

[…] For Y-STR loci, allele frequencies and gene diversity were calculated using PowerMarker v3.25 []. Haplotype frequencies, random match probabilities (sum of squares) and haplotype diversity were calculated using Arlequin Software v3.5 []. The discrimination capacity (DC) was determined as the proportion of different haplotypes in each sample []. A cluster structure of Y-STR haplotypes was generated using the YHRD database (http://www.yhrd.org/). To compare data from the studied Liaoning Han population with other published data, genetic distance (Rst statistics) was measured by analysis of molecular variance (AMOVA) and visualized using two multi-dimensional scaling (MDS) Rst plots via YHRD online tools (http://www.yhrd.org/Analyse/AMOVA).For autosomal loci, sample allele frequencies and exact Hardy-Weinberg equilibrium (HWE) tests were calculated using PowerMarker v3.25 []. Values for power of discrimination (DP), polymorphism information content (PIC), power of exclusion (PE), and heterozygosity (He) were calculated using Power Stats v1.2 software [] that had been modified by Raquel, et al. to support and manage the large amount of samples []. Pairwise genetic distance (Fst) and p values for each locus were calculated between populations using Arlequin v3.5 software []. Furthermore, Nei’s standard genetic distance between populations was generated by the Phylip 3.69 package [] and visualized with Treeview software []. Because the published relevant data is limited, the included groups for population comparison between Y-STR and autosomal STR are different. […]

Pipeline specifications

Software tools PowerMarker, Arlequin, PHYLIP, TreeViewX
Applications Phylogenetics, Population genetic analysis
Organisms Homo sapiens