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Detailed information for vg0721070672:

Variant ID: vg0721070672 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 21070672
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.88, T: 0.12, others allele: 0.00, population size: 105. )

Flanking Sequence (100 bp) in Reference Genome:

GTATTTTTCGGACATTCCGAAAACTTTTCGGACAAGTCCGAAAACAACAACATCGTTCTGGATGTTCTCGGAAAAGTCCGAAAATCACTTTCGGACAAGT[T/C]
CGAAAATATACAGAAGCGAAATTGACTCTACTGATGATTTTCAGAAAATCCAAAAATCAGTTTCGGACAAGTCCGAAAATATACAGAACCACTTTTGCCT

Reverse complement sequence

AGGCAAAAGTGGTTCTGTATATTTTCGGACTTGTCCGAAACTGATTTTTGGATTTTCTGAAAATCATCAGTAGAGTCAATTTCGCTTCTGTATATTTTCG[A/G]
ACTTGTCCGAAAGTGATTTTCGGACTTTTCCGAGAACATCCAGAACGATGTTGTTGTTTTCGGACTTGTCCGAAAAGTTTTCGGAATGTCCGAAAAATAC

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	25.60%	24.40%	1.21%	48.77%	NA
All Indica	2759	9.50%	11.90%	0.87%	77.78%	NA
All Japonica	1512	57.10%	39.50%	2.05%	1.39%	NA
Aus	269	3.30%	70.60%	0.37%	25.65%	NA
Indica I	595	5.20%	10.10%	0.84%	83.87%	NA
Indica II	465	15.50%	6.20%	1.29%	76.99%	NA
Indica III	913	10.20%	15.20%	0.66%	73.93%	NA
Indica Intermediate	786	8.30%	12.70%	0.89%	78.12%	NA
Temperate Japonica	767	62.30%	32.70%	4.04%	0.91%	NA
Tropical Japonica	504	40.90%	58.50%	0.00%	0.60%	NA
Japonica Intermediate	241	74.30%	21.20%	0.00%	4.56%	NA
VI/Aromatic	96	52.10%	11.50%	0.00%	36.46%	NA
Intermediate	90	31.10%	30.00%	1.11%	37.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0721070672	T -> DEL	N	N	silent_mutation	Average:10.588; most accessible tissue: Callus, score: 26.875	N	N	N	N
vg0721070672	T -> C	LOC_Os07g35190.1	upstream_gene_variant ; 2503.0bp to feature; MODIFIER	silent_mutation	Average:10.588; most accessible tissue: Callus, score: 26.875	N	N	N	N
vg0721070672	T -> C	LOC_Os07g35200.1	upstream_gene_variant ; 3568.0bp to feature; MODIFIER	silent_mutation	Average:10.588; most accessible tissue: Callus, score: 26.875	N	N	N	N
vg0721070672	T -> C	LOC_Os07g35180-LOC_Os07g35190	intergenic_region ; MODIFIER	silent_mutation	Average:10.588; most accessible tissue: Callus, score: 26.875	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0721070672	9.42E-06	NA	mr1142	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
vg0721070672	2.07E-06	2.12E-08	mr1165_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
vg0721070672	NA	9.40E-06	mr1477_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