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Detailed information for vg0307401131:

Variant ID: vg0307401131 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 7401131
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:

ACAAGAATATGCTAGCACAAACAGCAACTAGACCTATAGTGGCTCAAACAAGCAAAGCTAGTGGAGAGGGAGGAAGTAAAGTCACCAAAGATGAAGCTCA[C/T]
GAAGTTGTTCCCGAAGTTCGAATCCTTGAGGGGATTCTACTCTCCGTTGAGAAGCTCACTAAGAGCCGGGTCTTAGCTAACCTTTTTCCTCAAGAGGTTG

Reverse complement sequence

CAACCTCTTGAGGAAAAAGGTTAGCTAAGACCCGGCTCTTAGTGAGCTTCTCAACGGAGAGTAGAATCCCCTCAAGGATTCGAACTTCGGGAACAACTTC[G/A]
TGAGCTTCATCTTTGGTGACTTTACTTCCTCCCTCTCCACTAGCTTTGCTTGTTTGAGCCACTATAGGTCTAGTTGCTGTTTGTGCTAGCATATTCTTGT

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	74.10%	0.60%	11.34%	13.97%	NA
All Indica	2759	64.90%	0.90%	18.16%	15.98%	NA
All Japonica	1512	88.80%	0.00%	0.66%	10.58%	NA
Aus	269	92.60%	0.00%	3.72%	3.72%	NA
Indica I	595	48.10%	0.50%	27.39%	24.03%	NA
Indica II	465	51.40%	1.10%	19.78%	27.74%	NA
Indica III	913	84.10%	1.60%	10.95%	3.29%	NA
Indica Intermediate	786	63.40%	0.40%	18.58%	17.68%	NA
Temperate Japonica	767	83.80%	0.00%	0.78%	15.38%	NA
Tropical Japonica	504	91.70%	0.00%	0.60%	7.74%	NA
Japonica Intermediate	241	98.30%	0.00%	0.41%	1.24%	NA
VI/Aromatic	96	55.20%	2.10%	8.33%	34.38%	NA
Intermediate	90	73.30%	1.10%	7.78%	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
vg0307401131	C -> T	LOC_Os03g13670.1	upstream_gene_variant ; 4205.0bp to feature; MODIFIER	silent_mutation	Average:7.931; most accessible tissue: Minghui63 flag leaf, score: 11.122	N	N	N	N
vg0307401131	C -> T	LOC_Os03g13680.1	upstream_gene_variant ; 316.0bp to feature; MODIFIER	silent_mutation	Average:7.931; most accessible tissue: Minghui63 flag leaf, score: 11.122	N	N	N	N
vg0307401131	C -> T	LOC_Os03g13690.1	downstream_gene_variant ; 3239.0bp to feature; MODIFIER	silent_mutation	Average:7.931; most accessible tissue: Minghui63 flag leaf, score: 11.122	N	N	N	N
vg0307401131	C -> T	LOC_Os03g13680-LOC_Os03g13690	intergenic_region ; MODIFIER	silent_mutation	Average:7.931; most accessible tissue: Minghui63 flag leaf, score: 11.122	N	N	N	N
vg0307401131	C -> DEL	N	N	silent_mutation	Average:7.931; most accessible tissue: Minghui63 flag leaf, score: 11.122	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0307401131	2.06E-06	2.06E-06	mr1323	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
vg0307401131	4.96E-06	NA	mr1439	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