Sentence examples for based on core SNPs from inspiring English sources
The size of the genomes varied from 3.86 to 4.03 Mb.> A maximum-likelihood tree of the 8 sequenced genomes and 16 reported A. baumannii complete genomes were created based on core SNPs from whole-genome alignment.
Maximum likelihood phylogenetic analysis based on core genome SNPs of the ST239 isolates was performed using the RAxML BlackBox [ 32].
A phylogenetic tree of the 51 VRE from stool and 45 hospital isolates based on core genome SNPs showed that carriage isolates from the three study participants were interspersed throughout the tree (Fig. 2a).
A phylogenetic tree of the 51 VRE and 25 VSE isolates based on core genome SNPs is shown in Additional file 2. This showed that the VSE carried by P7 and P15 were closely related to their resident VRE populations demonstrating possible in vivo acquisition or loss of resistance, whilst as expected the VSE carried by P31 was not closely related to their VRE.
The division into two distinct clades is also well supported by a maximum likelihood phylogeny, and a split decomposition phylogenetic network based on all core SNPs in the pan genome (additional file 2), which indicates that phylogenetic signal that supports subdivision of S. enterica subsp. enterica is not limited to the 93 randomly selected loci, but instead is present genome-wide.
This research group demonstrated the global geographic distribution of the ST239 lineage, indicating intercontinental transmission, based on core-genome single nucleotide polymorphisms (SNPs) [ 9].
Analysis of protein-complex cores is essential for the algorithms based on Core-Attachments assumption.
A phylogenetic tree for the 51 VRE isolates based on SNPs in the core genome is shown in Fig. 1b.
Thus, the phylogenetic tree created based on SNPs of the core-genome showed that the genomic sequence of K. pneumoniae subsp. ozaenae is very different from that of the other K. pneumonia strains.
Based on the other SNPs, this SNP could be imputed.
