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Detailed information for vg0224775878:

Variant ID: vg0224775878 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 24775878
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.94, T: 0.07, others allele: 0.00, population size: 195. )

Flanking Sequence (100 bp) in Reference Genome:

AATAAGTTGCTGACACATTATATATTTATTTTAATTAACGGAACCATCTATGTTTATTTATTTATCTCTCTTCCTCGCGTTGCGTGGACCAGCTTCCCCT[C/T]
GTGTTGTATCTGTGGGCCCAACTTCTTAGAGTTCGTGAGCAGCTCGGCGACTAAATAGTCGCCCACTCACCTTCCTTCTTTCCTCCAGCGCATCACGCGA

Reverse complement sequence

TCGCGTGATGCGCTGGAGGAAAGAAGGAAGGTGAGTGGGCGACTATTTAGTCGCCGAGCTGCTCACGAACTCTAAGAAGTTGGGCCCACAGATACAACAC[G/A]
AGGGGAAGCTGGTCCACGCAACGCGAGGAAGAGAGATAAATAAATAAACATAGATGGTTCCGTTAATTAAAATAAATATATAATGTGTCAGCAACTTATT

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	50.00%	50.00%	0.04%	0.00%	NA
All Indica	2759	26.20%	73.70%	0.04%	0.00%	NA
All Japonica	1512	94.90%	5.10%	0.00%	0.00%	NA
Aus	269	24.20%	75.80%	0.00%	0.00%	NA
Indica I	595	3.20%	96.80%	0.00%	0.00%	NA
Indica II	465	18.70%	81.10%	0.22%	0.00%	NA
Indica III	913	43.60%	56.40%	0.00%	0.00%	NA
Indica Intermediate	786	28.00%	72.00%	0.00%	0.00%	NA
Temperate Japonica	767	94.40%	5.60%	0.00%	0.00%	NA
Tropical Japonica	504	93.80%	6.20%	0.00%	0.00%	NA
Japonica Intermediate	241	98.80%	1.20%	0.00%	0.00%	NA
VI/Aromatic	96	87.50%	12.50%	0.00%	0.00%	NA
Intermediate	90	60.00%	38.90%	1.11%	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
vg0224775878	C -> T	LOC_Os02g40870.1	upstream_gene_variant ; 838.0bp to feature; MODIFIER	silent_mutation	Average:71.113; most accessible tissue: Zhenshan97 panicle, score: 82.888	N	N	N	N
vg0224775878	C -> T	LOC_Os02g40890.1	upstream_gene_variant ; 4688.0bp to feature; MODIFIER	silent_mutation	Average:71.113; most accessible tissue: Zhenshan97 panicle, score: 82.888	N	N	N	N
vg0224775878	C -> T	LOC_Os02g40870.2	upstream_gene_variant ; 798.0bp to feature; MODIFIER	silent_mutation	Average:71.113; most accessible tissue: Zhenshan97 panicle, score: 82.888	N	N	N	N
vg0224775878	C -> T	LOC_Os02g40860.1	downstream_gene_variant ; 3128.0bp to feature; MODIFIER	silent_mutation	Average:71.113; most accessible tissue: Zhenshan97 panicle, score: 82.888	N	N	N	N
vg0224775878	C -> T	LOC_Os02g40880.1	downstream_gene_variant ; 1849.0bp to feature; MODIFIER	silent_mutation	Average:71.113; most accessible tissue: Zhenshan97 panicle, score: 82.888	N	N	N	N
vg0224775878	C -> T	LOC_Os02g40880.2	downstream_gene_variant ; 1849.0bp to feature; MODIFIER	silent_mutation	Average:71.113; most accessible tissue: Zhenshan97 panicle, score: 82.888	N	N	N	N
vg0224775878	C -> T	LOC_Os02g40870-LOC_Os02g40880	intergenic_region ; MODIFIER	silent_mutation	Average:71.113; most accessible tissue: Zhenshan97 panicle, score: 82.888	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0224775878	2.35E-06	NA	mr1099_2	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
vg0224775878	7.54E-07	NA	mr1099_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
vg0224775878	3.30E-06	NA	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