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Detailed information for vg0410965624:

Variant ID: vg0410965624 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 10965624
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: 103. )

Flanking Sequence (100 bp) in Reference Genome:

ATTTAGCATGTTGATTTTATAACTTTCTTTTATTTTATTTCTTTAGAAACCCGCTGTTCAAAAGTACAAAACTTGTGACCTTGTTTTCAACTGTTTCAAC[T/C]
TACCTTGCAAGCTTGGTTTACTTTATTTACTTACCTTCTTACTTTGATTTTCTAAACTTTATTCCAATTTGATCCAAAAACTTGTGCTATTAATTGGATA

Reverse complement sequence

TATCCAATTAATAGCACAAGTTTTTGGATCAAATTGGAATAAAGTTTAGAAAATCAAAGTAAGAAGGTAAGTAAATAAAGTAAACCAAGCTTGCAAGGTA[A/G]
GTTGAAACAGTTGAAAACAAGGTCACAAGTTTTGTACTTTTGAACAGCGGGTTTCTAAAGAAATAAAATAAAAGAAAGTTATAAAATCAACATGCTAAAT

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	31.20%	6.20%	33.22%	29.37%	NA
All Indica	2759	7.10%	10.40%	42.91%	39.62%	NA
All Japonica	1512	63.00%	0.00%	20.70%	16.34%	NA
Aus	269	94.80%	0.00%	4.46%	0.74%	NA
Indica I	595	3.00%	10.60%	36.81%	49.58%	NA
Indica II	465	4.70%	8.80%	44.52%	41.94%	NA
Indica III	913	9.00%	14.20%	50.93%	25.85%	NA
Indica Intermediate	786	9.30%	6.70%	37.28%	46.69%	NA
Temperate Japonica	767	96.10%	0.00%	0.65%	3.26%	NA
Tropical Japonica	504	9.50%	0.00%	53.97%	36.51%	NA
Japonica Intermediate	241	69.30%	0.00%	14.94%	15.77%	NA
VI/Aromatic	96	37.50%	0.00%	42.71%	19.79%	NA
Intermediate	90	41.10%	6.70%	22.22%	30.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0410965624	T -> C	LOC_Os04g19650.1	upstream_gene_variant ; 135.0bp to feature; MODIFIER	silent_mutation	Average:13.381; most accessible tissue: Zhenshan97 panicle, score: 20.424	N	N	N	N
vg0410965624	T -> C	LOC_Os04g19660.1	upstream_gene_variant ; 1201.0bp to feature; MODIFIER	silent_mutation	Average:13.381; most accessible tissue: Zhenshan97 panicle, score: 20.424	N	N	N	N
vg0410965624	T -> C	LOC_Os04g19640-LOC_Os04g19650	intergenic_region ; MODIFIER	silent_mutation	Average:13.381; most accessible tissue: Zhenshan97 panicle, score: 20.424	N	N	N	N
vg0410965624	T -> DEL	N	N	silent_mutation	Average:13.381; most accessible tissue: Zhenshan97 panicle, score: 20.424	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0410965624	7.43E-07	7.43E-07	mr1276_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