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Detailed information for vg0315759840:

Variant ID: vg0315759840 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 15759840
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.01, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:

CCCCTCACTTGTGAGGGCTGCTGGTTCTATTCCAATCATTTGTGTCCTTGGCTTGCTCTCTCTCTAGCACTTTTGAGCCTTGCTTTCTTGTTTCCCCTCT[C/T]
ACCCGTGTTCGATTTGGATTTGGTGTGTGTGTGAGAGTGGTGGATTCGAGTTTGTGTGAGTGCTTGTTGTTGACTTCGTGAAGATTTGTGAGCACTTGCA

Reverse complement sequence

TGCAAGTGCTCACAAATCTTCACGAAGTCAACAACAAGCACTCACACAAACTCGAATCCACCACTCTCACACACACACCAAATCCAAATCGAACACGGGT[G/A]
AGAGGGGAAACAAGAAAGCAAGGCTCAAAAGTGCTAGAGAGAGAGCAAGCCAAGGACACAAATGATTGGAATAGAACCAGCAGCCCTCACAAGTGAGGGG

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	67.10%	4.00%	19.40%	9.50%	NA
All Indica	2759	57.30%	1.30%	27.08%	14.35%	NA
All Japonica	1512	81.90%	8.30%	7.61%	2.18%	NA
Aus	269	73.60%	8.20%	13.75%	4.46%	NA
Indica I	595	55.00%	0.20%	35.80%	9.08%	NA
Indica II	465	64.10%	0.00%	26.45%	9.46%	NA
Indica III	913	57.50%	2.10%	20.70%	19.72%	NA
Indica Intermediate	786	54.80%	1.90%	28.24%	15.01%	NA
Temperate Japonica	767	98.40%	0.30%	0.78%	0.52%	NA
Tropical Japonica	504	55.80%	22.20%	17.46%	4.56%	NA
Japonica Intermediate	241	83.80%	5.00%	8.71%	2.49%	NA
VI/Aromatic	96	90.60%	5.20%	4.17%	0.00%	NA
Intermediate	90	72.20%	3.30%	15.56%	8.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0315759840	C -> T	LOC_Os03g27460.1	upstream_gene_variant ; 3734.0bp to feature; MODIFIER	silent_mutation	Average:12.046; most accessible tissue: Zhenshan97 panicle, score: 16.188	N	N	N	N
vg0315759840	C -> T	LOC_Os03g27460.2	upstream_gene_variant ; 3734.0bp to feature; MODIFIER	silent_mutation	Average:12.046; most accessible tissue: Zhenshan97 panicle, score: 16.188	N	N	N	N
vg0315759840	C -> T	LOC_Os03g27460.3	upstream_gene_variant ; 3734.0bp to feature; MODIFIER	silent_mutation	Average:12.046; most accessible tissue: Zhenshan97 panicle, score: 16.188	N	N	N	N
vg0315759840	C -> T	LOC_Os03g27470.1	downstream_gene_variant ; 964.0bp to feature; MODIFIER	silent_mutation	Average:12.046; most accessible tissue: Zhenshan97 panicle, score: 16.188	N	N	N	N
vg0315759840	C -> T	LOC_Os03g27480.1	downstream_gene_variant ; 3562.0bp to feature; MODIFIER	silent_mutation	Average:12.046; most accessible tissue: Zhenshan97 panicle, score: 16.188	N	N	N	N
vg0315759840	C -> T	LOC_Os03g27480.2	downstream_gene_variant ; 3722.0bp to feature; MODIFIER	silent_mutation	Average:12.046; most accessible tissue: Zhenshan97 panicle, score: 16.188	N	N	N	N
vg0315759840	C -> T	LOC_Os03g27470-LOC_Os03g27480	intergenic_region ; MODIFIER	silent_mutation	Average:12.046; most accessible tissue: Zhenshan97 panicle, score: 16.188	N	N	N	N
vg0315759840	C -> DEL	N	N	silent_mutation	Average:12.046; most accessible tissue: Zhenshan97 panicle, score: 16.188	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0315759840	1.13E-07	3.85E-08	mr1563_2	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