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Detailed information for vg0802472650:

Variant ID: vg0802472650 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 2472650
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 304. )

Flanking Sequence (100 bp) in Reference Genome:

TCGCATGGTAGAAAAAACGGAGGAATAGGAAAAACACAGGATTTTGACAGGAATTGAAGTGTAAAACAGAGGATTGCAAAACACAGGAAAAACACAGGAA[T/C]
GATCGTTTGATTGGATCGCAGGAAAAACGCAGGAATCAGATGAGAGAGATAGACTCAAAGGAAATTTTCCAAGAGGTTGGAGCTCTTGCTAAATTTCCTC

Reverse complement sequence

GAGGAAATTTAGCAAGAGCTCCAACCTCTTGGAAAATTTCCTTTGAGTCTATCTCTCTCATCTGATTCCTGCGTTTTTCCTGCGATCCAATCAAACGATC[A/G]
TTCCTGTGTTTTTCCTGTGTTTTGCAATCCTCTGTTTTACACTTCAATTCCTGTCAAAATCCTGTGTTTTTCCTATTCCTCCGTTTTTTCTACCATGCGA

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	92.70%	5.00%	1.74%	0.49%	NA
All Indica	2759	99.70%	0.00%	0.11%	0.18%	NA
All Japonica	1512	79.60%	15.30%	5.03%	0.07%	NA
Aus	269	93.70%	0.00%	0.00%	6.32%	NA
Indica I	595	99.80%	0.00%	0.17%	0.00%	NA
Indica II	465	99.10%	0.00%	0.00%	0.86%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	99.60%	0.00%	0.25%	0.13%	NA
Temperate Japonica	767	75.00%	17.20%	7.82%	0.00%	NA
Tropical Japonica	504	82.30%	15.90%	1.59%	0.20%	NA
Japonica Intermediate	241	88.80%	7.90%	3.32%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	90.00%	6.70%	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
vg0802472650	T -> C	LOC_Os08g04860-LOC_Os08g04870	intergenic_region ; MODIFIER	silent_mutation	Average:25.794; most accessible tissue: Zhenshan97 flower, score: 38.669	N	N	N	N
vg0802472650	T -> DEL	N	N	silent_mutation	Average:25.794; most accessible tissue: Zhenshan97 flower, score: 38.669	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0802472650	4.80E-06	4.80E-06	mr1514_2	Jap_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