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Detailed information for vg0114130447:

Variant ID: vg0114130447 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 14130447
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:

CGGTTTAGTTCCTGGATGGAACCGACTAGTACAAATCGGAAAAACAGAACATTTCGTGAACATATGACATGCGTTGGTCATCCGTAAAATGTGCTAGCAC[A/G]
TCTGTTGAAAGATAGACCTCTGATTCGTACATGCGTCGGCCTCGTGGATGGACCAGGAGCTCAACATTCCTTAAGGTTGTTCTTTCAAACCCATACAAGG

Reverse complement sequence

CCTTGTATGGGTTTGAAAGAACAACCTTAAGGAATGTTGAGCTCCTGGTCCATCCACGAGGCCGACGCATGTACGAATCAGAGGTCTATCTTTCAACAGA[T/C]
GTGCTAGCACATTTTACGGATGACCAACGCATGTCATATGTTCACGAAATGTTCTGTTTTTCCGATTTGTACTAGTCGGTTCCATCCAGGAACTAAACCG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	39.20%	9.40%	13.29%	38.15%	NA
All Indica	2759	10.30%	15.20%	19.28%	55.16%	NA
All Japonica	1512	96.30%	0.70%	2.71%	0.33%	NA
Aus	269	4.10%	1.50%	5.95%	88.48%	NA
Indica I	595	15.10%	5.70%	21.68%	57.48%	NA
Indica II	465	19.10%	4.50%	13.33%	63.01%	NA
Indica III	913	3.20%	29.20%	17.96%	49.62%	NA
Indica Intermediate	786	9.80%	12.50%	22.52%	55.22%	NA
Temperate Japonica	767	98.40%	0.00%	1.43%	0.13%	NA
Tropical Japonica	504	92.10%	1.80%	5.56%	0.60%	NA
Japonica Intermediate	241	98.30%	0.40%	0.83%	0.41%	NA
VI/Aromatic	96	53.10%	5.20%	29.17%	12.50%	NA
Intermediate	90	55.60%	3.30%	12.22%	28.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0114130447	A -> G	LOC_Os01g25050.1	upstream_gene_variant ; 1211.0bp to feature; MODIFIER	silent_mutation	Average:10.929; most accessible tissue: Callus, score: 53.796	N	N	N	N
vg0114130447	A -> G	LOC_Os01g25060.1	upstream_gene_variant ; 395.0bp to feature; MODIFIER	silent_mutation	Average:10.929; most accessible tissue: Callus, score: 53.796	N	N	N	N
vg0114130447	A -> G	LOC_Os01g25040.1	downstream_gene_variant ; 2934.0bp to feature; MODIFIER	silent_mutation	Average:10.929; most accessible tissue: Callus, score: 53.796	N	N	N	N
vg0114130447	A -> G	LOC_Os01g25050-LOC_Os01g25060	intergenic_region ; MODIFIER	silent_mutation	Average:10.929; most accessible tissue: Callus, score: 53.796	N	N	N	N
vg0114130447	A -> DEL	N	N	silent_mutation	Average:10.929; most accessible tissue: Callus, score: 53.796	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0114130447	1.51E-08	1.12E-09	mr1197	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
vg0114130447	3.45E-07	3.45E-07	mr1197	Ind_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