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Detailed information for vg0224803813:

Variant ID: vg0224803813 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 24803813
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.00, others allele: 0.00, population size: 318. )

Flanking Sequence (100 bp) in Reference Genome:

ACACAACAGCATGACACATTCCTTCAGTACTTAATTAACTTTCACTATGTTAATGCCGCGGTGCCCATTGGATCCTTCTGGTCATAACACCTAAGTGGAC[C/T]
AGAATTGATAAGAACGCATATGATTTGACCCCAATTCAACTAGCGATATATGAAGCGTGGGCCCAATACGTGCAAAGAGGAGGCCTCAGGAAGACAGGAC

Reverse complement sequence

GTCCTGTCTTCCTGAGGCCTCCTCTTTGCACGTATTGGGCCCACGCTTCATATATCGCTAGTTGAATTGGGGTCAAATCATATGCGTTCTTATCAATTCT[G/A]
GTCCACTTAGGTGTTATGACCAGAAGGATCCAATGGGCACCGCGGCATTAACATAGTGAAAGTTAATTAAGTACTGAAGGAATGTGTCATGCTGTTGTGT

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	85.30%	13.50%	1.18%	0.00%	NA
All Indica	2759	86.70%	13.20%	0.11%	0.00%	NA
All Japonica	1512	88.60%	8.10%	3.31%	0.00%	NA
Aus	269	50.90%	48.30%	0.74%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	77.40%	22.60%	0.00%	0.00%	NA
Indica III	913	83.00%	16.90%	0.11%	0.00%	NA
Indica Intermediate	786	86.40%	13.40%	0.25%	0.00%	NA
Temperate Japonica	767	89.80%	5.20%	4.95%	0.00%	NA
Tropical Japonica	504	92.50%	6.50%	0.99%	0.00%	NA
Japonica Intermediate	241	76.80%	20.30%	2.90%	0.00%	NA
VI/Aromatic	96	79.20%	19.80%	1.04%	0.00%	NA
Intermediate	90	94.40%	5.60%	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
vg0224803813	C -> T	LOC_Os02g40940.1	upstream_gene_variant ; 3508.0bp to feature; MODIFIER	silent_mutation	Average:24.217; most accessible tissue: Callus, score: 48.417	N	N	N	N
vg0224803813	C -> T	LOC_Os02g40930.1	intron_variant ; MODIFIER	silent_mutation	Average:24.217; most accessible tissue: Callus, score: 48.417	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0224803813	NA	3.27E-07	mr1077	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
vg0224803813	4.49E-06	4.75E-06	mr1913	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
vg0224803813	NA	1.52E-07	mr1962	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
vg0224803813	NA	3.57E-06	mr1150_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
vg0224803813	NA	9.72E-06	mr1479_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
vg0224803813	4.42E-06	2.00E-06	mr1613_2	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
vg0224803813	NA	4.11E-07	mr1871_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