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Detailed information for vg0707346462:

Variant ID: vg0707346462 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 7346462
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 42. )

Flanking Sequence (100 bp) in Reference Genome:

TTGAGCCACTATCACCCTAGGTTTGCAAAACATAACTTAGTTGCTTAGTTAGAGTTGACCCTCACCAAGCCTAGCAACTTAGGTTAGTTTTGATTAGGTG[T/A]
CATTTAGTTTTAAATCGTCTATTCACCCCCCTCTAGTCGACATCTCGATCCTATAGCAGGCGGCGGCGGCGGCGGCGGGCGGCGGCAGCGGGCTTGACTG

Reverse complement sequence

CAGTCAAGCCCGCTGCCGCCGCCCGCCGCCGCCGCCGCCGCCTGCTATAGGATCGAGATGTCGACTAGAGGGGGGTGAATAGACGATTTAAAACTAAATG[A/T]
CACCTAATCAAAACTAACCTAAGTTGCTAGGCTTGGTGAGGGTCAACTCTAACTAAGCAACTAAGTTATGTTTTGCAAACCTAGGGTGATAGTGGCTCAA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	57.80%	7.10%	28.82%	6.33%	NA
All Indica	2759	40.70%	12.00%	46.76%	0.58%	NA
All Japonica	1512	79.80%	0.00%	1.85%	18.39%	NA
Aus	269	98.50%	0.00%	1.49%	0.00%	NA
Indica I	595	26.10%	8.20%	65.71%	0.00%	NA
Indica II	465	47.50%	10.10%	41.08%	1.29%	NA
Indica III	913	37.70%	19.30%	42.06%	0.99%	NA
Indica Intermediate	786	51.10%	7.50%	41.22%	0.13%	NA
Temperate Japonica	767	96.10%	0.00%	0.65%	3.26%	NA
Tropical Japonica	504	67.70%	0.00%	2.78%	29.56%	NA
Japonica Intermediate	241	53.10%	0.00%	3.73%	43.15%	NA
VI/Aromatic	96	81.20%	0.00%	18.75%	0.00%	NA
Intermediate	90	66.70%	3.30%	24.44%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0707346462	T -> DEL	N	N	silent_mutation	Average:46.621; most accessible tissue: Minghui63 panicle, score: 64.459	N	N	N	N
vg0707346462	T -> A	LOC_Os07g12830.1	upstream_gene_variant ; 1292.0bp to feature; MODIFIER	silent_mutation	Average:46.621; most accessible tissue: Minghui63 panicle, score: 64.459	N	N	N	N
vg0707346462	T -> A	LOC_Os07g12830.2	upstream_gene_variant ; 1344.0bp to feature; MODIFIER	silent_mutation	Average:46.621; most accessible tissue: Minghui63 panicle, score: 64.459	N	N	N	N
vg0707346462	T -> A	LOC_Os07g12830.3	upstream_gene_variant ; 1344.0bp to feature; MODIFIER	silent_mutation	Average:46.621; most accessible tissue: Minghui63 panicle, score: 64.459	N	N	N	N
vg0707346462	T -> A	LOC_Os07g12820-LOC_Os07g12830	intergenic_region ; MODIFIER	silent_mutation	Average:46.621; most accessible tissue: Minghui63 panicle, score: 64.459	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0707346462	2.49E-06	5.71E-07	mr1756_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