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Detailed information for vg0714886064:

Variant ID: vg0714886064 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 14886064
Reference Allele: C	Alternative Allele: G
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, C: 0.01, others allele: 0.00, population size: 80. )

Flanking Sequence (100 bp) in Reference Genome:

CCATATATATAAGCTTTCAAAGTTTAAAATCCTGAAATTTGCAAAGACTACTACTCACTGTTTGAAAATTCGAATTTAGCTGTACATCTGCGTGATTTTT[C/G]
TGCAAGATTTATTCCAACCATTTTAAAGAGAACATCATGAGGATCACACTGAAATTTGGTTCATTCAAATCGGAGTTAAAATGAATTCCCTGTGATTTTT

Reverse complement sequence

AAAAATCACAGGGAATTCATTTTAACTCCGATTTGAATGAACCAAATTTCAGTGTGATCCTCATGATGTTCTCTTTAAAATGGTTGGAATAAATCTTGCA[G/C]
AAAAATCACGCAGATGTACAGCTAAATTCGAATTTTCAAACAGTGAGTAGTAGTCTTTGCAAATTTCAGGATTTTAAACTTTGAAAGCTTATATATATGG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	57.00%	39.90%	3.07%	0.00%	NA
All Indica	2759	82.20%	13.40%	4.46%	0.00%	NA
All Japonica	1512	6.90%	91.90%	1.12%	0.00%	NA
Aus	269	87.70%	10.80%	1.49%	0.00%	NA
Indica I	595	60.50%	25.50%	13.95%	0.00%	NA
Indica II	465	81.30%	18.30%	0.43%	0.00%	NA
Indica III	913	97.80%	2.10%	0.11%	0.00%	NA
Indica Intermediate	786	80.90%	14.40%	4.71%	0.00%	NA
Temperate Japonica	767	12.60%	85.10%	2.22%	0.00%	NA
Tropical Japonica	504	0.40%	99.60%	0.00%	0.00%	NA
Japonica Intermediate	241	2.50%	97.50%	0.00%	0.00%	NA
VI/Aromatic	96	53.10%	46.90%	0.00%	0.00%	NA
Intermediate	90	41.10%	57.80%	1.11%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0714886064	C -> G	LOC_Os07g25940.1	upstream_gene_variant ; 448.0bp to feature; MODIFIER	silent_mutation	Average:28.733; most accessible tissue: Callus, score: 83.777	N	N	N	N
vg0714886064	C -> G	LOC_Os07g25950.1	upstream_gene_variant ; 4805.0bp to feature; MODIFIER	silent_mutation	Average:28.733; most accessible tissue: Callus, score: 83.777	N	N	N	N
vg0714886064	C -> G	LOC_Os07g25930.1	downstream_gene_variant ; 2998.0bp to feature; MODIFIER	silent_mutation	Average:28.733; most accessible tissue: Callus, score: 83.777	N	N	N	N
vg0714886064	C -> G	LOC_Os07g25930-LOC_Os07g25940	intergenic_region ; MODIFIER	silent_mutation	Average:28.733; most accessible tissue: Callus, score: 83.777	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0714886064	2.26E-06	2.26E-06	mr1004_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0714886064	NA	7.58E-06	mr1161_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0714886064	1.99E-06	1.99E-06	mr1754_2	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