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Detailed information for vg1203908733:

Variant ID: vg1203908733 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 3908733
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 46. )

Flanking Sequence (100 bp) in Reference Genome:

ACCTGAAATGCAAAGTTGGGGTCGAAATTCAATGTCCCGTGGCTCTTTTATGCGAGAATATGATTTTGGTGATATTTGCAAATTCCGAATGCCATTCAAA[T/C]
AAATATCCCAAATGCAGAGGGTTATTTGTGTGTTTTTGGAAAATTCAGGGTTTAAAGTGCAAAGATTCCAATGCAGAGGAACATGCACTTAATTTCCAAA

Reverse complement sequence

TTTGGAAATTAAGTGCATGTTCCTCTGCATTGGAATCTTTGCACTTTAAACCCTGAATTTTCCAAAAACACACAAATAACCCTCTGCATTTGGGATATTT[A/G]
TTTGAATGGCATTCGGAATTTGCAAATATCACCAAAATCATATTCTCGCATAAAAGAGCCACGGGACATTGAATTTCGACCCCAACTTTGCATTTCAGGT

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	33.00%	0.20%	0.25%	66.57%	NA
All Indica	2759	2.20%	0.30%	0.33%	97.21%	NA
All Japonica	1512	89.40%	0.00%	0.07%	10.58%	NA
Aus	269	7.40%	0.00%	0.37%	92.19%	NA
Indica I	595	1.30%	0.30%	0.34%	97.98%	NA
Indica II	465	2.40%	0.20%	0.43%	96.99%	NA
Indica III	913	1.90%	0.10%	0.22%	97.81%	NA
Indica Intermediate	786	3.20%	0.40%	0.38%	96.06%	NA
Temperate Japonica	767	98.70%	0.00%	0.13%	1.17%	NA
Tropical Japonica	504	77.80%	0.00%	0.00%	22.22%	NA
Japonica Intermediate	241	83.80%	0.00%	0.00%	16.18%	NA
VI/Aromatic	96	78.10%	0.00%	0.00%	21.88%	NA
Intermediate	90	58.90%	1.10%	1.11%	38.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1203908733	T -> C	LOC_Os12g07760.1	upstream_gene_variant ; 403.0bp to feature; MODIFIER	silent_mutation	Average:28.967; most accessible tissue: Callus, score: 80.476	N	N	N	N
vg1203908733	T -> C	LOC_Os12g07750-LOC_Os12g07760	intergenic_region ; MODIFIER	silent_mutation	Average:28.967; most accessible tissue: Callus, score: 80.476	N	N	N	N
vg1203908733	T -> DEL	N	N	silent_mutation	Average:28.967; most accessible tissue: Callus, score: 80.476	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1203908733	1.66E-06	1.76E-06	mr1095	Jap_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
vg1203908733	NA	1.32E-08	mr1302	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
vg1203908733	NA	4.81E-19	mr1304	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
vg1203908733	NA	1.90E-16	mr1323	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
vg1203908733	NA	8.17E-11	mr1325	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
vg1203908733	NA	3.68E-35	mr1350	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
vg1203908733	NA	1.86E-14	mr1361	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
vg1203908733	NA	7.05E-13	mr1386	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
vg1203908733	4.31E-07	5.80E-32	mr1414	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
vg1203908733	2.88E-06	1.92E-06	mr1414	Jap_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
vg1203908733	NA	1.55E-07	mr1439	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
vg1203908733	NA	2.94E-06	mr1527	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
vg1203908733	NA	2.22E-06	mr1682	Jap_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
vg1203908733	NA	9.60E-08	mr1690	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
vg1203908733	NA	6.37E-07	mr1810	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