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Detailed information for vg0902337033:

Variant ID: vg0902337033 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 2337033
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.78, T: 0.22, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:

CTAATAATCTGCTACGCGGTGTAGTGGTGCCTCTCAACAACTCAGCCAAATGGAGCACCTTACCAAGCTCTTACGAGTGTCTTACCAACAATGCTAAGGA[C/T]
GGCATAACTTGTGGTTGGTTCATGACACATTGAAGGACATGATGTGGCGATTGCAAGGATTAAAGTGGTGCTGGCCAGAAGTATATATGTGAAGCTTGGG

Reverse complement sequence

CCCAAGCTTCACATATATACTTCTGGCCAGCACCACTTTAATCCTTGCAATCGCCACATCATGTCCTTCAATGTGTCATGAACCAACCACAAGTTATGCC[G/A]
TCCTTAGCATTGTTGGTAAGACACTCGTAAGAGCTTGGTAAGGTGCTCCATTTGGCTGAGTTGTTGAGAGGCACCACTACACCGCGTAGCAGATTATTAG

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	63.70%	23.60%	0.63%	12.15%	NA
All Indica	2759	96.10%	3.20%	0.07%	0.65%	NA
All Japonica	1512	2.10%	63.20%	1.85%	32.94%	NA
Aus	269	99.30%	0.40%	0.00%	0.37%	NA
Indica I	595	95.10%	4.40%	0.00%	0.50%	NA
Indica II	465	92.00%	7.70%	0.00%	0.22%	NA
Indica III	913	99.10%	0.10%	0.11%	0.66%	NA
Indica Intermediate	786	95.80%	3.10%	0.13%	1.02%	NA
Temperate Japonica	767	1.20%	96.20%	0.39%	2.22%	NA
Tropical Japonica	504	2.40%	19.00%	4.17%	74.40%	NA
Japonica Intermediate	241	4.10%	50.20%	1.66%	43.98%	NA
VI/Aromatic	96	9.40%	47.90%	0.00%	42.71%	NA
Intermediate	90	55.60%	26.70%	0.00%	17.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0902337033	C -> DEL	N	N	silent_mutation	Average:62.215; most accessible tissue: Callus, score: 73.141	N	N	N	N
vg0902337033	C -> T	LOC_Os09g04410.1	downstream_gene_variant ; 1796.0bp to feature; MODIFIER	silent_mutation	Average:62.215; most accessible tissue: Callus, score: 73.141	N	N	N	N
vg0902337033	C -> T	LOC_Os09g04410-LOC_Os09g04420	intergenic_region ; MODIFIER	silent_mutation	Average:62.215; most accessible tissue: Callus, score: 73.141	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0902337033	NA	3.08E-07	mr1190	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
vg0902337033	NA	3.53E-15	mr1228	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
vg0902337033	NA	4.87E-07	mr1072_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
vg0902337033	NA	5.79E-07	mr1075_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
vg0902337033	NA	1.16E-07	mr1200_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
vg0902337033	3.52E-06	3.52E-06	mr1234_2	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