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Detailed information for vg0402263913:

Variant ID: vg0402263913 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 2263913
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, T: 0.04, others allele: 0.00, population size: 82. )

Flanking Sequence (100 bp) in Reference Genome:

AAGAATATGCTTTTCGATATCCTCGTTCCTTTCTCCAGCGATCACTTAAATAGTCTTACAAAAGGGTAAGGACCACATTCATCGTGGCCTCAGTTTCAGA[T/C]
AGCTGTTTACATAACTAAGTTCAGGAAAACGACAATGATTACATTAACAGTGGCCACCGACAAAGATGGACGGCCAGATGATGTTCATACCGCTTTGCTC

Reverse complement sequence

GAGCAAAGCGGTATGAACATCATCTGGCCGTCCATCTTTGTCGGTGGCCACTGTTAATGTAATCATTGTCGTTTTCCTGAACTTAGTTATGTAAACAGCT[A/G]
TCTGAAACTGAGGCCACGATGAATGTGGTCCTTACCCTTTTGTAAGACTATTTAAGTGATCGCTGGAGAAAGGAACGAGGATATCGAAAAGCATATTCTT

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	29.30%	13.80%	0.28%	56.67%	NA
All Indica	2759	23.30%	2.10%	0.33%	74.19%	NA
All Japonica	1512	30.80%	37.90%	0.13%	31.22%	NA
Aus	269	78.80%	2.60%	0.74%	17.84%	NA
Indica I	595	3.40%	2.50%	0.50%	93.61%	NA
Indica II	465	3.20%	1.70%	0.22%	94.84%	NA
Indica III	913	47.50%	0.20%	0.11%	52.14%	NA
Indica Intermediate	786	22.30%	4.30%	0.51%	72.90%	NA
Temperate Japonica	767	24.00%	67.30%	0.13%	8.60%	NA
Tropical Japonica	504	33.30%	3.60%	0.20%	62.90%	NA
Japonica Intermediate	241	46.90%	16.20%	0.00%	36.93%	NA
VI/Aromatic	96	28.10%	0.00%	0.00%	71.88%	NA
Intermediate	90	38.90%	14.40%	0.00%	46.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0402263913	T -> C	LOC_Os04g04700.1	upstream_gene_variant ; 3551.0bp to feature; MODIFIER	silent_mutation	Average:6.183; most accessible tissue: Callus, score: 16.674	N	N	N	N
vg0402263913	T -> C	LOC_Os04g04710.1	upstream_gene_variant ; 539.0bp to feature; MODIFIER	silent_mutation	Average:6.183; most accessible tissue: Callus, score: 16.674	N	N	N	N
vg0402263913	T -> C	LOC_Os04g04720.1	upstream_gene_variant ; 2971.0bp to feature; MODIFIER	silent_mutation	Average:6.183; most accessible tissue: Callus, score: 16.674	N	N	N	N
vg0402263913	T -> C	LOC_Os04g04710-LOC_Os04g04720	intergenic_region ; MODIFIER	silent_mutation	Average:6.183; most accessible tissue: Callus, score: 16.674	N	N	N	N
vg0402263913	T -> DEL	N	N	silent_mutation	Average:6.183; most accessible tissue: Callus, score: 16.674	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0402263913	3.30E-06	NA	mr1067	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
vg0402263913	NA	2.32E-06	mr1100	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
vg0402263913	NA	1.22E-09	mr1108	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
vg0402263913	NA	5.73E-07	mr1111	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
vg0402263913	NA	2.15E-08	mr1112	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
vg0402263913	NA	6.89E-07	mr1286	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
vg0402263913	NA	1.37E-07	mr1777	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