Fig. 3
From: Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters
Phylogenetic analysis and nucleic acid differences of family clusters’ virus sequences compared to the other SARS-CoV-2 virus sequences from Yogyakarta and Central Java. a The tree was constructed from 29.409 nt length of the open reading frame (ORF) of 142 SARS-CoV-2 virus sequences using Neighbor Joining statistical method and computed using the Kimura 2-parameter method with 2,000 bootstrap replications. The tree is rooted to Wuhan/Hu-1/2019 (NC_045512.2) with the bootstrap percentage values less than 70% hidden and it is drawn to scale (0.0001) with branch lengths measured in the number of substitutions per site. b The number of base differences per sequence from between sequences are shown. Codon positions included were 1st + 2nd + 3rd + Noncoding. All ambiguous positions were removed for each sequence pair. There was a total of 29,409 positions in the final dataset. Family clusters are indicated in asterisks: Case-1 (*) and Case-2 (**)