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Detailed information for vg0408655352:

Variant ID: vg0408655352 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 8655352
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.80, T: 0.20, others allele: 0.00, population size: 104. )

Flanking Sequence (100 bp) in Reference Genome:

ACCATGCACCCCGAGCCCAGCCTAAAACCATTTTGAGGATTTTGAATAGAGGGGGAGGTGTGAATCCGATTCCACAATAATCCAACCATTCCATAGTGTC[T/C]
AGGTGACATGAATATTCCCAAAGTCTAGAGTTGTAAAACCACCTAATGTTGCCTAATTAAACAGCGAAGCATCTACCTAAATTCATACTAGTGGTACCAT

Reverse complement sequence

ATGGTACCACTAGTATGAATTTAGGTAGATGCTTCGCTGTTTAATTAGGCAACATTAGGTGGTTTTACAACTCTAGACTTTGGGAATATTCATGTCACCT[A/G]
GACACTATGGAATGGTTGGATTATTGTGGAATCGGATTCACACCTCCCCCTCTATTCAAAATCCTCAAAATGGTTTTAGGCTGGGCTCGGGGTGCATGGT

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	64.40%	35.20%	0.42%	0.00%	NA
All Indica	2759	97.60%	2.10%	0.33%	0.00%	NA
All Japonica	1512	1.50%	98.00%	0.46%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	98.00%	1.70%	0.34%	0.00%	NA
Indica II	465	96.60%	3.20%	0.22%	0.00%	NA
Indica III	913	98.60%	1.00%	0.44%	0.00%	NA
Indica Intermediate	786	96.70%	3.10%	0.25%	0.00%	NA
Temperate Japonica	767	0.40%	99.60%	0.00%	0.00%	NA
Tropical Japonica	504	2.00%	98.00%	0.00%	0.00%	NA
Japonica Intermediate	241	4.10%	92.90%	2.90%	0.00%	NA
VI/Aromatic	96	16.70%	82.30%	1.04%	0.00%	NA
Intermediate	90	48.90%	47.80%	3.33%	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
vg0408655352	T -> C	LOC_Os04g15930.1	upstream_gene_variant ; 259.0bp to feature; MODIFIER	silent_mutation	Average:9.755; most accessible tissue: Zhenshan97 root, score: 16.934	N	N	N	N
vg0408655352	T -> C	LOC_Os04g15944.1	downstream_gene_variant ; 1931.0bp to feature; MODIFIER	silent_mutation	Average:9.755; most accessible tissue: Zhenshan97 root, score: 16.934	N	N	N	N
vg0408655352	T -> C	LOC_Os04g15930-LOC_Os04g15944	intergenic_region ; MODIFIER	silent_mutation	Average:9.755; most accessible tissue: Zhenshan97 root, score: 16.934	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0408655352	NA	1.20E-09	mr1089	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
vg0408655352	NA	4.34E-11	mr1454	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
vg0408655352	NA	4.49E-06	mr1844	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
vg0408655352	NA	3.50E-06	mr1977	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
vg0408655352	NA	2.42E-32	mr1310_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
vg0408655352	4.73E-06	6.66E-06	mr1310_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
vg0408655352	1.10E-06	1.10E-06	mr1778_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
vg0408655352	NA	1.44E-14	mr1959_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