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Detailed information for vg1203289460:

Variant ID: vg1203289460 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 3289460
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.95, T: 0.05, others allele: 0.00, population size: 126. )

Flanking Sequence (100 bp) in Reference Genome:

TTCGGGCCGGCGGTGGCACTCCTAGGGGTTGATGGATCAAGGATGTGGCCGATCTGGTGAGGTGTTGCTCACCGCCAGGTTGCCGTTGGGAACCCTGCTC[C/T]
GGCTCCATGTTGACATCCCATGTGGTGCCCGAGCTCCGCACAGTCATCTATTCTATCTAAATTAATTTATAAGAAAATATAAATTCAAATCAAGGAATAT

Reverse complement sequence

ATATTCCTTGATTTGAATTTATATTTTCTTATAAATTAATTTAGATAGAATAGATGACTGTGCGGAGCTCGGGCACCACATGGGATGTCAACATGGAGCC[G/A]
GAGCAGGGTTCCCAACGGCAACCTGGCGGTGAGCAACACCTCACCAGATCGGCCACATCCTTGATCCATCAACCCCTAGGAGTGCCACCGCCGGCCCGAA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	75.40%	24.30%	0.06%	0.23%	NA
All Indica	2759	65.40%	34.10%	0.11%	0.33%	NA
All Japonica	1512	99.30%	0.70%	0.00%	0.00%	NA
Aus	269	51.70%	48.30%	0.00%	0.00%	NA
Indica I	595	81.00%	18.70%	0.17%	0.17%	NA
Indica II	465	56.10%	43.70%	0.00%	0.22%	NA
Indica III	913	60.50%	38.90%	0.11%	0.55%	NA
Indica Intermediate	786	64.90%	34.70%	0.13%	0.25%	NA
Temperate Japonica	767	99.50%	0.50%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	97.90%	2.10%	0.00%	0.00%	NA
VI/Aromatic	96	63.50%	36.50%	0.00%	0.00%	NA
Intermediate	90	65.60%	32.20%	0.00%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1203289460	C -> DEL	N	N	silent_mutation	Average:68.025; most accessible tissue: Zhenshan97 flag leaf, score: 80.156	N	N	N	N
vg1203289460	C -> T	LOC_Os12g06780.1	upstream_gene_variant ; 4066.0bp to feature; MODIFIER	silent_mutation	Average:68.025; most accessible tissue: Zhenshan97 flag leaf, score: 80.156	N	N	N	N
vg1203289460	C -> T	LOC_Os12g06750.1	downstream_gene_variant ; 4301.0bp to feature; MODIFIER	silent_mutation	Average:68.025; most accessible tissue: Zhenshan97 flag leaf, score: 80.156	N	N	N	N
vg1203289460	C -> T	LOC_Os12g06760.1	downstream_gene_variant ; 1078.0bp to feature; MODIFIER	silent_mutation	Average:68.025; most accessible tissue: Zhenshan97 flag leaf, score: 80.156	N	N	N	N
vg1203289460	C -> T	LOC_Os12g06770.1	intron_variant ; MODIFIER	silent_mutation	Average:68.025; most accessible tissue: Zhenshan97 flag leaf, score: 80.156	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1203289460	9.49E-06	9.49E-06	mr1337	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
vg1203289460	NA	1.06E-08	mr1644	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
vg1203289460	NA	1.27E-12	mr1553_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
vg1203289460	NA	7.82E-08	mr1553_2	Ind_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
vg1203289460	NA	2.12E-08	mr1974_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