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Detailed information for vg1004688821:

Variant ID: vg1004688821 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 4688821
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.75, C: 0.24, others allele: 0.00, population size: 173. )

Flanking Sequence (100 bp) in Reference Genome:

ACGTCGAGGGCCTTCAGGTGGTATAAGTCGAAGACTTCCTTGTGCCGGATCCAAATAACATCTTCTCCTTGGTAATAATTTGAGTTTCGCACCCTAGCTC[T/C]
GAACATCTCTCTACCCATCGCTGATTTGTCCATGTACCATTGATGGAACCGGTACATCTGTGTAGGTAGCTCTCTGATCTTATCAGGCGTGACTAGCGGT

Reverse complement sequence

ACCGCTAGTCACGCCTGATAAGATCAGAGAGCTACCTACACAGATGTACCGGTTCCATCAATGGTACATGGACAAATCAGCGATGGGTAGAGAGATGTTC[A/G]
GAGCTAGGGTGCGAAACTCAAATTATTACCAAGGAGAAGATGTTATTTGGATCCGGCACAAGGAAGTCTTCGACTTATACCACCTGAAGGCCCTCGACGT

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	53.40%	43.30%	3.36%	0.00%	NA
All Indica	2759	41.90%	54.00%	4.13%	0.00%	NA
All Japonica	1512	82.30%	17.30%	0.40%	0.00%	NA
Aus	269	10.00%	86.60%	3.35%	0.00%	NA
Indica I	595	41.80%	57.60%	0.50%	0.00%	NA
Indica II	465	46.20%	52.30%	1.51%	0.00%	NA
Indica III	913	41.40%	49.90%	8.65%	0.00%	NA
Indica Intermediate	786	39.80%	57.00%	3.18%	0.00%	NA
Temperate Japonica	767	84.90%	15.10%	0.00%	0.00%	NA
Tropical Japonica	504	85.50%	14.30%	0.20%	0.00%	NA
Japonica Intermediate	241	67.20%	30.70%	2.07%	0.00%	NA
VI/Aromatic	96	39.60%	34.40%	26.04%	0.00%	NA
Intermediate	90	65.60%	28.90%	5.56%	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
vg1004688821	T -> C	LOC_Os10g08650.1	missense_variant ; p.Arg382Gly; MODERATE	nonsynonymous_codon ; R382G	Average:20.04; most accessible tissue: Callus, score: 40.103	unknown	unknown	TOLERATED	1.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1004688821	NA	8.23E-06	mr1308_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
vg1004688821	8.65E-06	8.69E-06	mr1703_2	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