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Detailed information for vg0223674836:

Variant ID: vg0223674836 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 23674836
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: 286. )

Flanking Sequence (100 bp) in Reference Genome:

ACATGCCCTTACTCTATCAAATCAAATAAATGAGCATGTACACCAAGTATGTATACCAAGCACGAAGGGAGATATTATCTTTGAGATCACAGGCAGAGAA[C/T]
GCTCCCTTTGAGATTGAAGCCTTTTATTGACTTCCACCTACAATTTAGCTACCTTTTGCTTCCTAAGCTGCTCATGGAACTTGTTGGTTAGTGACAATCT

Reverse complement sequence

AGATTGTCACTAACCAACAAGTTCCATGAGCAGCTTAGGAAGCAAAAGGTAGCTAAATTGTAGGTGGAAGTCAATAAAAGGCTTCAATCTCAAAGGGAGC[G/A]
TTCTCTGCCTGTGATCTCAAAGATAATATCTCCCTTCGTGCTTGGTATACATACTTGGTGTACATGCTCATTTATTTGATTTGATAGAGTAAGGGCATGT

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	82.40%	17.20%	0.19%	0.25%	NA
All Indica	2759	72.30%	27.30%	0.07%	0.36%	NA
All Japonica	1512	98.70%	0.80%	0.46%	0.07%	NA
Aus	269	85.10%	14.90%	0.00%	0.00%	NA
Indica I	595	71.80%	28.20%	0.00%	0.00%	NA
Indica II	465	86.00%	13.50%	0.00%	0.43%	NA
Indica III	913	59.10%	40.40%	0.00%	0.44%	NA
Indica Intermediate	786	79.80%	19.50%	0.25%	0.51%	NA
Temperate Japonica	767	98.30%	0.90%	0.78%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	97.50%	1.70%	0.41%	0.41%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	91.10%	7.80%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0223674836	C -> T	LOC_Os02g39200.1	upstream_gene_variant ; 2509.0bp to feature; MODIFIER	silent_mutation	Average:33.581; most accessible tissue: Zhenshan97 young leaf, score: 48.658	N	N	N	N
vg0223674836	C -> T	LOC_Os02g39190.1	intron_variant ; MODIFIER	silent_mutation	Average:33.581; most accessible tissue: Zhenshan97 young leaf, score: 48.658	N	N	N	N
vg0223674836	C -> DEL	N	N	silent_mutation	Average:33.581; most accessible tissue: Zhenshan97 young leaf, score: 48.658	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0223674836	NA	8.84E-06	mr1929	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
vg0223674836	4.35E-06	7.28E-07	mr1063_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
vg0223674836	9.26E-07	NA	mr1962_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