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Detailed information for vg1002291312:

Variant ID: vg1002291312 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 2291312
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.91, C: 0.08, others allele: 0.00, population size: 200. )

Flanking Sequence (100 bp) in Reference Genome:

AAGATAAATATATGTAAACTGAATAAAATTCTAAAAGGAAGCAATATTCCTCCAAACAGTATATTCATAAACCTTGTAACTAGGGGGTGCATAAGTTATC[T/C]
AAAATTATTCTGTGCAAGTAATCACTAGTATGTAAATGGACTAGAGTAATACATCCTGAAGCTAACATAATCTAGTAAAAAATAGAACTTCATTGACCAA

Reverse complement sequence

TTGGTCAATGAAGTTCTATTTTTTACTAGATTATGTTAGCTTCAGGATGTATTACTCTAGTCCATTTACATACTAGTGATTACTTGCACAGAATAATTTT[A/G]
GATAACTTATGCACCCCCTAGTTACAAGGTTTATGAATATACTGTTTGGAGGAATATTGCTTCCTTTTAGAATTTTATTCAGTTTACATATATTTATCTT

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	67.10%	32.50%	0.02%	0.40%	NA
All Indica	2759	60.30%	39.00%	0.00%	0.65%	NA
All Japonica	1512	84.70%	15.20%	0.07%	0.00%	NA
Aus	269	24.50%	75.50%	0.00%	0.00%	NA
Indica I	595	69.70%	29.70%	0.00%	0.50%	NA
Indica II	465	65.80%	33.30%	0.00%	0.86%	NA
Indica III	913	51.90%	47.80%	0.00%	0.33%	NA
Indica Intermediate	786	59.70%	39.30%	0.00%	1.02%	NA
Temperate Japonica	767	91.50%	8.30%	0.13%	0.00%	NA
Tropical Japonica	504	78.00%	22.00%	0.00%	0.00%	NA
Japonica Intermediate	241	77.20%	22.80%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	70.00%	28.90%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1002291312	T -> C	LOC_Os10g04770.1	intron_variant ; MODIFIER	silent_mutation	Average:38.044; most accessible tissue: Callus, score: 70.976	N	N	N	N
vg1002291312	T -> DEL	N	N	silent_mutation	Average:38.044; most accessible tissue: Callus, score: 70.976	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1002291312	NA	9.88E-06	mr1179	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
vg1002291312	2.71E-08	NA	mr1486	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
vg1002291312	NA	1.91E-09	mr1486	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
vg1002291312	NA	1.16E-09	mr1510	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
vg1002291312	2.70E-07	NA	mr1548	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
vg1002291312	NA	1.41E-07	mr1548	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
vg1002291312	2.44E-06	NA	mr1588	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
vg1002291312	NA	6.41E-08	mr1588	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
vg1002291312	1.39E-06	3.65E-13	mr1624	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
vg1002291312	NA	6.62E-08	mr1624	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
vg1002291312	5.62E-06	NA	mr1751	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
vg1002291312	2.28E-06	NA	mr1486_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
vg1002291312	NA	9.05E-08	mr1486_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
vg1002291312	NA	7.92E-10	mr1624_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
vg1002291312	NA	3.96E-07	mr1721_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