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Detailed information for vg0503490446:

Variant ID: vg0503490446 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 3490446
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.01, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:

TTTTTGCATTTTAGATATAACAAGAATTCAGAATGACTAAGCTGCCATTTGCAATCTATTGCGGCTTGAACCAAGCATTTTGAATTACTCCCAGGGCTAG[T/C]
AATGTGTTCTTTTTTTCTGTAGGGTCATATTTTACTATGTTAATCTTATCGGCTTTTTAACGTTTCACTTTTGGTTAAGCTTTTTCAGTTTTTGATGTTG

Reverse complement sequence

CAACATCAAAAACTGAAAAAGCTTAACCAAAAGTGAAACGTTAAAAAGCCGATAAGATTAACATAGTAAAATATGACCCTACAGAAAAAAAGAACACATT[A/G]
CTAGCCCTGGGAGTAATTCAAAATGCTTGGTTCAAGCCGCAATAGATTGCAAATGGCAGCTTAGTCATTCTGAATTCTTGTTATATCTAAAATGCAAAAA

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	91.90%	7.80%	0.23%	0.00%	NA
All Indica	2759	86.40%	13.30%	0.33%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	99.30%	0.00%	0.74%	0.00%	NA
Indica I	595	97.30%	2.50%	0.17%	0.00%	NA
Indica II	465	88.80%	11.20%	0.00%	0.00%	NA
Indica III	913	78.30%	21.20%	0.44%	0.00%	NA
Indica Intermediate	786	86.00%	13.50%	0.51%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	96.70%	3.30%	0.00%	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
vg0503490446	T -> C	LOC_Os05g06710.1	downstream_gene_variant ; 2170.0bp to feature; MODIFIER	silent_mutation	Average:45.206; most accessible tissue: Callus, score: 79.623	N	N	N	N
vg0503490446	T -> C	LOC_Os05g06700.1	intron_variant ; MODIFIER	silent_mutation	Average:45.206; most accessible tissue: Callus, score: 79.623	N	N	N	N
vg0503490446	T -> C	LOC_Os05g06700.2	intron_variant ; MODIFIER	silent_mutation	Average:45.206; most accessible tissue: Callus, score: 79.623	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0503490446	NA	1.57E-06	mr1792	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
vg0503490446	NA	2.88E-06	mr1456_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
vg0503490446	4.68E-06	1.98E-06	mr1577_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
vg0503490446	5.51E-06	7.95E-07	mr1577_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
vg0503490446	NA	5.08E-06	mr1587_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
vg0503490446	8.48E-06	4.56E-07	mr1792_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
vg0503490446	NA	2.19E-06	mr1792_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
vg0503490446	3.23E-06	NA	mr1803_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
vg0503490446	7.85E-06	9.35E-07	mr1803_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
vg0503490446	NA	3.36E-06	mr1932_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