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Detailed information for vg0802945643:

Variant ID: vg0802945643 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 2945643
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.51, T: 0.50, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:

GAGGTGAATCCATTTTTCCCCTTTCCTCTCTCCTTTAGCCACCGCCACCACCCATCACCGCCACCCACCATTGCCGGCCGAAGAGAGCTCTTGTTGTCGC[C/T]
GTTCCGGCATCCTCCCTCTCCCTCTCTGCCAGCTACCGCCTTCCCTGGATACGCGGTACTCGGGAACATCACCCGACACCGGCGTCGCCGTCTTCCAACT

Reverse complement sequence

AGTTGGAAGACGGCGACGCCGGTGTCGGGTGATGTTCCCGAGTACCGCGTATCCAGGGAAGGCGGTAGCTGGCAGAGAGGGAGAGGGAGGATGCCGGAAC[G/A]
GCGACAACAAGAGCTCTCTTCGGCCGGCAATGGTGGGTGGCGGTGATGGGTGGTGGCGGTGGCTAAAGGAGAGAGGAAAGGGGAAAAATGGATTCACCTC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	64.00%	35.20%	0.70%	0.04%	NA
All Indica	2759	62.70%	36.70%	0.54%	0.04%	NA
All Japonica	1512	76.10%	22.70%	1.12%	0.07%	NA
Aus	269	0.00%	100.00%	0.00%	0.00%	NA
Indica I	595	52.10%	46.90%	1.01%	0.00%	NA
Indica II	465	78.30%	21.10%	0.65%	0.00%	NA
Indica III	913	59.70%	40.00%	0.22%	0.11%	NA
Indica Intermediate	786	65.00%	34.50%	0.51%	0.00%	NA
Temperate Japonica	767	73.90%	24.40%	1.56%	0.13%	NA
Tropical Japonica	504	80.00%	19.40%	0.60%	0.00%	NA
Japonica Intermediate	241	75.10%	24.10%	0.83%	0.00%	NA
VI/Aromatic	96	85.40%	14.60%	0.00%	0.00%	NA
Intermediate	90	70.00%	28.90%	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
vg0802945643	C -> T	LOC_Os08g05520.1	downstream_gene_variant ; 2879.0bp to feature; MODIFIER	silent_mutation	Average:49.063; most accessible tissue: Zhenshan97 panicle, score: 71.253	N	N	N	N
vg0802945643	C -> T	LOC_Os08g05510-LOC_Os08g05520	intergenic_region ; MODIFIER	silent_mutation	Average:49.063; most accessible tissue: Zhenshan97 panicle, score: 71.253	N	N	N	N
vg0802945643	C -> DEL	N	N	silent_mutation	Average:49.063; most accessible tissue: Zhenshan97 panicle, score: 71.253	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0802945643	8.97E-06	NA	mr1826	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
vg0802945643	NA	3.40E-08	mr1707_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