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Detailed information for vg0624880130:

Variant ID: vg0624880130 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 24880130
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.01, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:

AAACTTATTTTACAAACAGATCCTAAAAAAACTTATTTCGGGAATGAAACTTTTTCGTGAGCGCCAACGTCATTGGTGTCGTGGTCTTGATGGTGAGCTC[T/G]
GCGTAGCGAAGGGCAACGAGCTCCATGGTGGATGTGCTCCTCGATGGTGCACGGTGGCGGTGGATCTCTATTTTCTTCCCCCTCTCTTTTTCCACTTTCT

Reverse complement sequence

AGAAAGTGGAAAAAGAGAGGGGGAAGAAAATAGAGATCCACCGCCACCGTGCACCATCGAGGAGCACATCCACCATGGAGCTCGTTGCCCTTCGCTACGC[A/C]
GAGCTCACCATCAAGACCACGACACCAATGACGTTGGCGCTCACGAAAAAGTTTCATTCCCGAAATAAGTTTTTTTAGGATCTGTTTGTAAAATAAGTTT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	49.40%	22.70%	6.07%	21.84%	NA
All Indica	2759	26.70%	32.70%	8.95%	31.61%	NA
All Japonica	1512	92.50%	1.40%	1.06%	5.09%	NA
Aus	269	21.90%	48.30%	7.43%	22.30%	NA
Indica I	595	65.90%	7.70%	5.71%	20.67%	NA
Indica II	465	9.20%	47.10%	13.55%	30.11%	NA
Indica III	913	11.90%	43.00%	7.67%	37.35%	NA
Indica Intermediate	786	24.60%	31.20%	10.18%	34.10%	NA
Temperate Japonica	767	95.30%	0.40%	1.83%	2.48%	NA
Tropical Japonica	504	84.70%	3.40%	0.40%	11.51%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	85.40%	2.10%	1.04%	11.46%	NA
Intermediate	90	66.70%	16.70%	3.33%	13.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0624880130	T -> G	LOC_Os06g41500.1	upstream_gene_variant ; 720.0bp to feature; MODIFIER	silent_mutation	Average:42.422; most accessible tissue: Zhenshan97 panicle, score: 83.41	N	N	N	N
vg0624880130	T -> G	LOC_Os06g41500-LOC_Os06g41510	intergenic_region ; MODIFIER	silent_mutation	Average:42.422; most accessible tissue: Zhenshan97 panicle, score: 83.41	N	N	N	N
vg0624880130	T -> DEL	N	N	silent_mutation	Average:42.422; most accessible tissue: Zhenshan97 panicle, score: 83.41	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0624880130	NA	8.87E-06	mr1011	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
vg0624880130	NA	3.11E-08	mr1749	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
vg0624880130	NA	6.07E-06	mr1749	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
vg0624880130	NA	1.14E-08	mr1449_2	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