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Detailed information for vg0335650235:

Variant ID: vg0335650235 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 35650235
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 291. )

Flanking Sequence (100 bp) in Reference Genome:

TAGGCTAGTAGTTTAATTTCAAAACAAAGGTAACTCATGGTTGTTGCATATCTTTTGATCTGTAACTTGATAATAATTGGTACAATTCTCCAAAGCAAAA[T/C]
ACAGTGTGTAGCTTCATATACAGAATCAGGCGCACAATTAGTCTTGGATATTGCAGAAACAATTAGTTTGCATTTCAATAGGATAAATTTGTTACCAAAA

Reverse complement sequence

TTTTGGTAACAAATTTATCCTATTGAAATGCAAACTAATTGTTTCTGCAATATCCAAGACTAATTGTGCGCCTGATTCTGTATATGAAGCTACACACTGT[A/G]
TTTTGCTTTGGAGAATTGTACCAATTATTATCAAGTTACAGATCAAAAGATATGCAACAACCATGAGTTACCTTTGTTTTGAAATTAAACTACTAGCCTA

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	94.20%	4.70%	1.10%	0.00%	NA
All Indica	2759	99.90%	0.10%	0.04%	0.00%	NA
All Japonica	1512	82.70%	14.10%	3.17%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.80%	0.00%	0.17%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	99.90%	0.10%	0.00%	0.00%	NA
Temperate Japonica	767	95.80%	1.60%	2.61%	0.00%	NA
Tropical Japonica	504	66.70%	30.60%	2.78%	0.00%	NA
Japonica Intermediate	241	74.70%	19.50%	5.81%	0.00%	NA
VI/Aromatic	96	97.90%	1.00%	1.04%	0.00%	NA
Intermediate	90	92.20%	5.60%	2.22%	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
vg0335650235	T -> C	LOC_Os03g63050.1	upstream_gene_variant ; 3770.0bp to feature; MODIFIER	silent_mutation	Average:39.69; most accessible tissue: Callus, score: 66.775	N	N	N	N
vg0335650235	T -> C	LOC_Os03g63040.1	intron_variant ; MODIFIER	silent_mutation	Average:39.69; most accessible tissue: Callus, score: 66.775	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0335650235	NA	5.44E-06	mr1543	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
vg0335650235	NA	1.85E-06	mr1596	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
vg0335650235	NA	2.54E-07	mr1668	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
vg0335650235	4.59E-09	7.05E-19	mr1871	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
vg0335650235	NA	2.16E-08	mr1871	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
vg0335650235	NA	2.20E-06	mr1880	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
vg0335650235	NA	1.38E-13	mr1742_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
vg0335650235	NA	1.94E-20	mr1871_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