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Detailed information for vg0718107373:

Variant ID: vg0718107373 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 18107373
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.54, C: 0.46, others allele: 0.00, population size: 100. )

Flanking Sequence (100 bp) in Reference Genome:

GTCCAACCGTTTGCATGACGCGTACAACGCGCGGTCGCACGTCTCTATGAAAGTACTTTGGAGAACAGGGTTTGTCTCCTTTTATAGCGTATTCTAACTT[T/C]
TGACTTGGGATTTAGCCTCTCAAAAAAGGGCATCTTTCCCCGAAAAAAAAGGGGCATCTTGATAAAGAACCCCTTATGGTAGCCTAGCTAATTACTTATA

Reverse complement sequence

TATAAGTAATTAGCTAGGCTACCATAAGGGGTTCTTTATCAAGATGCCCCTTTTTTTTCGGGGAAAGATGCCCTTTTTTGAGAGGCTAAATCCCAAGTCA[A/G]
AAGTTAGAATACGCTATAAAAGGAGACAAACCCTGTTCTCCAAAGTACTTTCATAGAGACGTGCGACCGCGCGTTGTACGCGTCATGCAAACGGTTGGAC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	62.20%	37.30%	0.15%	0.32%	NA
All Indica	2759	46.30%	53.00%	0.18%	0.51%	NA
All Japonica	1512	87.20%	12.70%	0.07%	0.00%	NA
Aus	269	68.80%	30.90%	0.37%	0.00%	NA
Indica I	595	23.70%	75.50%	0.34%	0.50%	NA
Indica II	465	76.30%	22.60%	0.22%	0.86%	NA
Indica III	913	39.90%	59.80%	0.11%	0.22%	NA
Indica Intermediate	786	53.20%	46.10%	0.13%	0.64%	NA
Temperate Japonica	767	99.50%	0.50%	0.00%	0.00%	NA
Tropical Japonica	504	68.80%	31.00%	0.20%	0.00%	NA
Japonica Intermediate	241	86.70%	13.30%	0.00%	0.00%	NA
VI/Aromatic	96	92.70%	6.20%	0.00%	1.04%	NA
Intermediate	90	75.60%	24.40%	0.00%	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
vg0718107373	T -> DEL	N	N	silent_mutation	Average:37.088; most accessible tissue: Callus, score: 59.031	N	N	N	N
vg0718107373	T -> C	LOC_Os07g30590.1	upstream_gene_variant ; 3658.0bp to feature; MODIFIER	silent_mutation	Average:37.088; most accessible tissue: Callus, score: 59.031	N	N	N	N
vg0718107373	T -> C	LOC_Os07g30600.1	intron_variant ; MODIFIER	silent_mutation	Average:37.088; most accessible tissue: Callus, score: 59.031	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0718107373	NA	1.92E-06	mr1480	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
vg0718107373	4.18E-07	NA	mr1692	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
vg0718107373	1.16E-06	1.04E-07	mr1692	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
vg0718107373	NA	3.78E-06	mr1968	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
vg0718107373	1.60E-06	NA	mr1480_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
vg0718107373	1.26E-08	1.49E-09	mr1480_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
vg0718107373	NA	1.17E-06	mr1711_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
vg0718107373	NA	5.06E-10	mr1968_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