Additionally, 38 individuals with close relationships with other study individuals (estimated genome-wide identity-by-descent proportion of alleles shared >0.20) were excluded from further analysis. The final WGS panel contains genotypes from 2,874 individuals at 26.85M SNVs, 1.59M indels, and 11.88...
The GBDP scores were calculated with the Genome-to-Genome Distance Calculator (GGDC) 3.0 [58, 59]. The values from Formula 2, one of three formulas (Formula 1, based on high-scoring segment pairs per total length; Formula 2, based on identity per high-scoring segment pairs; and Formula...
$GVCF_GENOMICS_DB_WORK_PATH gatk GenotypeGVCFs \ --reference $(find $REF_GENOME_PATH -maxdepth 5 -name "*Mtb_H37Rv.genomic.fna") \ --variant gendb://$GVCF_GENOMICS_DB_WORK_PATH \ --use-new-qual-calculator \ --output $GATK_JOINT_CALL_COHORT_VCF_FILE_PATH/'joint_call_cohort.vcf...
Unique genome A total of 4421 (31.54%) proteins do not display any sig- nificant identity with selected myxobacteria, which are mentioned as unique proteins in M. rosea (Table S2a). Among them, only 347 unique proteins have been func- tionally identified which are associated with the COG ...
MSA ID calculator calculates identity matrix of more than 11,000 sequences with a sequence length of 2,696 base pairs in less than 100 seconds. Tree and Distance Matrix calculation tools generate phylogenetic tree and distance matrix, respectively, using neighbor joining% identity and BLOSUM 62 ...
Where\({cross}\)represents the cross product of two matrices,\({eye}(3)\)represents the 3×3 identity matrix,\({matrix\_}\exp\)represents the matrix exponential function, and\({axi}{s}_{{end}}\)is calculated as follows: $${axi}{s}_{{end}}=\frac{{axi}{s}_{{temp}}}{\paral...
Average nucleotide identity AT: Acyltransferase C: Condensation domain CFS: Cell-free supernatant sample DDH: DNA-DNA hybridization ESI: Electrospray ionization FA: Fatty acid GGDC: Genome to genome distance calculator KR: Keto reductase KS: Ketosynthase MLSA: Multi-locus sequence analys...
* name of the method is percentage of identity, the DistanceMatrix contains * the fractional dissimilarity (D), computed as D = 1 - PID. * * It is recommended to use the method * {@linkDistanceMatrixCalculator#fractionalDissimilarity(MultipleSequenceAlignment)} * instead...
Using Uniprot, the R-M system in B43P8 was found to have the largest percentage identity to a restriction endonuclease (REase) (85% identity) and methyltransferase (MTase) (88.9% identity) in Selenomonas sputigena, an anaerobic Gram-negative bacteria. Cluster C Four prophages were identified in...
Only 14 of the IGC genes gave matches to the genome when requiring ≥95% identity and ≥70% of the IGC gene’s bases aligned. However, this gene catalog is mainly derived from samples from adults, while SFB in most animals peak in young individuals during weaning46. Therefore, we instead...