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Detailed information for vg0233648723:

Variant ID: vg0233648723 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 33648723
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, others allele: 0.00, population size: 336. )

Flanking Sequence (100 bp) in Reference Genome:

GAGATCATCTCCAAGAGTAATAAGCACCGAGATGACAGCCCACGAGATATTCCAAGTGCTCACCCAAGATCCTAGTCTTCACACATCTCCAAATCTTCCT[C/T]
TCTCCCTCTCAATCTCTCTTTCTCACAAGAATTAGGCTCTAGATTGAGTGGAGATGGCAAGAAACACTTAGGAGAGGCTAGCAACAGCTCTAGGGATGAA

Reverse complement sequence

TTCATCCCTAGAGCTGTTGCTAGCCTCTCCTAAGTGTTTCTTGCCATCTCCACTCAATCTAGAGCCTAATTCTTGTGAGAAAGAGAGATTGAGAGGGAGA[G/A]
AGGAAGATTTGGAGATGTGTGAAGACTAGGATCTTGGGTGAGCACTTGGAATATCTCGTGGGCTGTCATCTCGGTGCTTATTACTCTTGGAGATGATCTC

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	88.80%	11.20%	0.00%	0.00%	NA
All Indica	2759	81.10%	18.90%	0.00%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	91.40%	8.60%	0.00%	0.00%	NA
Indica II	465	83.00%	17.00%	0.00%	0.00%	NA
Indica III	913	74.20%	25.80%	0.00%	0.00%	NA
Indica Intermediate	786	80.20%	19.80%	0.00%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	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	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
vg0233648723	C -> T	LOC_Os02g54940.1	upstream_gene_variant ; 1956.0bp to feature; MODIFIER	silent_mutation	Average:23.733; most accessible tissue: Minghui63 flower, score: 33.389	N	N	N	N
vg0233648723	C -> T	LOC_Os02g54930.1	downstream_gene_variant ; 4415.0bp to feature; MODIFIER	silent_mutation	Average:23.733; most accessible tissue: Minghui63 flower, score: 33.389	N	N	N	N
vg0233648723	C -> T	LOC_Os02g54930-LOC_Os02g54940	intergenic_region ; MODIFIER	silent_mutation	Average:23.733; most accessible tissue: Minghui63 flower, score: 33.389	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0233648723	3.29E-06	NA	mr1955	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
vg0233648723	3.82E-06	3.82E-06	mr1955	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