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Detailed information for vg0729492205:

Variant ID: vg0729492205 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 29492205
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTATTATTATATGGTTTATTTAAGGTGAAATCCACTGTGTTAAATTCGCTTGGATATATTTTTTGTTAGAAAATTATGAGCTGTAATTAGGAGTCCCACC[G/A]
TCTCAAGTTTGCGAGTTTTTTAAAGAGATTTCTTGTACGATTTCTTTTGTATTTTCAAAAGCGAACAAACTTAAAACATGACTCGTACACGGATAACGTA

Reverse complement sequence

TACGTTATCCGTGTACGAGTCATGTTTTAAGTTTGTTCGCTTTTGAAAATACAAAAGAAATCGTACAAGAAATCTCTTTAAAAAACTCGCAAACTTGAGA[C/T]
GGTGGGACTCCTAATTACAGCTCATAATTTTCTAACAAAAAATATATCCAAGCGAATTTAACACAGTGGATTTCACCTTAAATAAACCATATAATAATAA

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	53.30%	46.30%	0.34%	0.00%	NA
All Indica	2759	75.10%	24.60%	0.22%	0.00%	NA
All Japonica	1512	16.30%	83.30%	0.46%	0.00%	NA
Aus	269	58.70%	40.50%	0.74%	0.00%	NA
Indica I	595	93.90%	5.70%	0.34%	0.00%	NA
Indica II	465	87.70%	12.00%	0.22%	0.00%	NA
Indica III	913	58.30%	41.60%	0.11%	0.00%	NA
Indica Intermediate	786	73.00%	26.70%	0.25%	0.00%	NA
Temperate Japonica	767	0.80%	99.10%	0.13%	0.00%	NA
Tropical Japonica	504	31.90%	67.10%	0.99%	0.00%	NA
Japonica Intermediate	241	32.80%	66.80%	0.41%	0.00%	NA
VI/Aromatic	96	9.40%	90.60%	0.00%	0.00%	NA
Intermediate	90	38.90%	60.00%	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
vg0729492205	G -> A	LOC_Os07g49260.1	upstream_gene_variant ; 3709.0bp to feature; MODIFIER	silent_mutation	Average:50.414; most accessible tissue: Callus, score: 78.477	N	N	N	N
vg0729492205	G -> A	LOC_Os07g49240.1	downstream_gene_variant ; 4767.0bp to feature; MODIFIER	silent_mutation	Average:50.414; most accessible tissue: Callus, score: 78.477	N	N	N	N
vg0729492205	G -> A	LOC_Os07g49250.1	downstream_gene_variant ; 32.0bp to feature; MODIFIER	silent_mutation	Average:50.414; most accessible tissue: Callus, score: 78.477	N	N	N	N
vg0729492205	G -> A	LOC_Os07g49250-LOC_Os07g49260	intergenic_region ; MODIFIER	silent_mutation	Average:50.414; most accessible tissue: Callus, score: 78.477	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0729492205	NA	9.63E-06	mr1133	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
vg0729492205	NA	1.87E-14	mr1218	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
vg0729492205	NA	2.66E-11	mr1352	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
vg0729492205	2.08E-06	NA	mr1559	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
vg0729492205	NA	5.89E-06	mr1602	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
vg0729492205	NA	7.59E-09	mr1696	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
vg0729492205	NA	1.03E-07	mr1063_2	Ind_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