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Detailed information for vg0224459717:

Variant ID: vg0224459717 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 24459717
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACCAGCGATAACAAGCTGATTTGGTTAAGCACATGCTGGGGTGGTTTTTGTAATAAAACATAATAGTGGATGTGCATTTACAATAAAATAACTTTATAGG[G/A]
TGAAATGTCAAACTTGAAGGTACTTCCGGTGTGTGTGTTTTTTACAATTTTCCCAACTTTAGTAGAAAAGGAGGTCCAAACTAAACAACACTCTATATAT

Reverse complement sequence

ATATATAGAGTGTTGTTTAGTTTGGACCTCCTTTTCTACTAAAGTTGGGAAAATTGTAAAAAACACACACACCGGAAGTACCTTCAAGTTTGACATTTCA[C/T]
CCTATAAAGTTATTTTATTGTAAATGCACATCCACTATTATGTTTTATTACAAAAACCACCCCAGCATGTGCTTAACCAAATCAGCTTGTTATCGCTGGT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	79.50%	2.50%	0.25%	17.82%	NA
All Indica	2759	84.70%	0.50%	0.07%	14.75%	NA
All Japonica	1512	68.30%	5.50%	0.60%	25.60%	NA
Aus	269	85.50%	3.00%	0.37%	11.15%	NA
Indica I	595	64.90%	0.00%	0.00%	35.13%	NA
Indica II	465	96.30%	0.00%	0.22%	3.44%	NA
Indica III	913	86.00%	1.00%	0.00%	13.03%	NA
Indica Intermediate	786	91.30%	0.50%	0.13%	8.02%	NA
Temperate Japonica	767	58.30%	9.30%	0.65%	31.81%	NA
Tropical Japonica	504	87.90%	1.20%	0.40%	10.52%	NA
Japonica Intermediate	241	59.30%	2.50%	0.83%	37.34%	NA
VI/Aromatic	96	85.40%	11.50%	0.00%	3.12%	NA
Intermediate	90	82.20%	1.10%	0.00%	16.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0224459717	G -> A	LOC_Os02g40390.1	upstream_gene_variant ; 1809.0bp to feature; MODIFIER	silent_mutation	Average:30.289; most accessible tissue: Callus, score: 71.891	N	N	N	N
vg0224459717	G -> A	LOC_Os02g40400.1	downstream_gene_variant ; 2531.0bp to feature; MODIFIER	silent_mutation	Average:30.289; most accessible tissue: Callus, score: 71.891	N	N	N	N
vg0224459717	G -> A	LOC_Os02g40390-LOC_Os02g40400	intergenic_region ; MODIFIER	silent_mutation	Average:30.289; most accessible tissue: Callus, score: 71.891	N	N	N	N
vg0224459717	G -> DEL	N	N	silent_mutation	Average:30.289; most accessible tissue: Callus, score: 71.891	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0224459717	1.07E-07	1.07E-07	mr1470	Jap_All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251