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Detailed information for vg0427734065:

Variant ID: vg0427734065 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 27734065
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:

GTCTTGTTGGTTGCATTGTCATAATGGCATCCGGGTTTTACATTTTTTAAAAAATATTGAGTGTACTCTGATGCTTTTTCTATAGTAAAAATGCACATTG[C/T]
ACACGAGCCGATGTCCGATTTTAAAAGAAAACAAAAATTTCAGGTTCATCACAATCACATGTTAGCTAATGTAATACTAAAAATTTTCATGTCAAAGTTA

Reverse complement sequence

TAACTTTGACATGAAAATTTTTAGTATTACATTAGCTAACATGTGATTGTGATGAACCTGAAATTTTTGTTTTCTTTTAAAATCGGACATCGGCTCGTGT[G/A]
CAATGTGCATTTTTACTATAGAAAAAGCATCAGAGTACACTCAATATTTTTTAAAAAATGTAAAACCCGGATGCCATTATGACAATGCAACCAACAAGAC

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	65.70%	33.70%	0.61%	0.00%	NA
All Indica	2759	42.00%	57.10%	0.91%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.07%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	19.70%	79.70%	0.67%	0.00%	NA
Indica II	465	78.50%	21.10%	0.43%	0.00%	NA
Indica III	913	32.90%	66.50%	0.66%	0.00%	NA
Indica Intermediate	786	48.00%	50.40%	1.65%	0.00%	NA
Temperate Japonica	767	99.70%	0.10%	0.13%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	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	77.80%	18.90%	3.33%	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
vg0427734065	C -> T	LOC_Os04g46780.2	3_prime_UTR_variant ; 253.0bp to feature; MODIFIER	silent_mutation	Average:50.76; most accessible tissue: Callus, score: 82.952	N	N	N	N
vg0427734065	C -> T	LOC_Os04g46800.1	upstream_gene_variant ; 4159.0bp to feature; MODIFIER	silent_mutation	Average:50.76; most accessible tissue: Callus, score: 82.952	N	N	N	N
vg0427734065	C -> T	LOC_Os04g46770.1	downstream_gene_variant ; 3012.0bp to feature; MODIFIER	silent_mutation	Average:50.76; most accessible tissue: Callus, score: 82.952	N	N	N	N
vg0427734065	C -> T	LOC_Os04g46790.1	downstream_gene_variant ; 2416.0bp to feature; MODIFIER	silent_mutation	Average:50.76; most accessible tissue: Callus, score: 82.952	N	N	N	N
vg0427734065	C -> T	LOC_Os04g46780.1	intron_variant ; MODIFIER	silent_mutation	Average:50.76; most accessible tissue: Callus, score: 82.952	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0427734065	NA	2.22E-07	mr1174	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
vg0427734065	NA	7.00E-06	mr1298	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
vg0427734065	NA	6.00E-07	mr1731	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
vg0427734065	NA	7.80E-09	mr1174_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
vg0427734065	NA	3.39E-08	mr1347_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
vg0427734065	NA	5.70E-06	mr1355_2	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