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Detailed information for vg0812497333:

Variant ID: vg0812497333 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 12497333
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AACCCAGAAGAGGAGTTCCTGGAAGATGAAGGCTTTGGTGTCTAGCTCGTGCCTGCTGTCAAGCGCCTGTGGTCATCGCCCTAGTCTTCCGCTGTTTCCC[G/A]
TTTGTCTTTGTGTGTGCTGGGCCTTCGCCGCCAATGTAATAAAGTAACTATTTATGCTTCCACTTGATAAACTCTGAAATGTATCAACTTTTGGTGTACC

Reverse complement sequence

GGTACACCAAAAGTTGATACATTTCAGAGTTTATCAAGTGGAAGCATAAATAGTTACTTTATTACATTGGCGGCGAAGGCCCAGCACACACAAAGACAAA[C/T]
GGGAAACAGCGGAAGACTAGGGCGATGACCACAGGCGCTTGACAGCAGGCACGAGCTAGACACCAAAGCCTTCATCTTCCAGGAACTCCTCTTCTGGGTT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	97.70%	1.10%	0.51%	0.68%	NA
All Indica	2759	98.40%	0.00%	0.69%	0.94%	NA
All Japonica	1512	95.80%	3.40%	0.33%	0.40%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	99.30%	0.00%	0.00%	0.67%	NA
Indica II	465	98.30%	0.00%	0.22%	1.51%	NA
Indica III	913	98.20%	0.00%	1.42%	0.33%	NA
Indica Intermediate	786	97.80%	0.00%	0.64%	1.53%	NA
Temperate Japonica	767	97.10%	1.60%	0.52%	0.78%	NA
Tropical Japonica	504	95.80%	4.00%	0.20%	0.00%	NA
Japonica Intermediate	241	91.70%	8.30%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	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
vg0812497333	G -> A	LOC_Os08g20800.1	upstream_gene_variant ; 4564.0bp to feature; MODIFIER	silent_mutation	Average:42.654; most accessible tissue: Zhenshan97 flag leaf, score: 66.327	N	N	N	N
vg0812497333	G -> A	LOC_Os08g20820.1	upstream_gene_variant ; 1756.0bp to feature; MODIFIER	silent_mutation	Average:42.654; most accessible tissue: Zhenshan97 flag leaf, score: 66.327	N	N	N	N
vg0812497333	G -> A	LOC_Os08g20840.1	upstream_gene_variant ; 3512.0bp to feature; MODIFIER	silent_mutation	Average:42.654; most accessible tissue: Zhenshan97 flag leaf, score: 66.327	N	N	N	N
vg0812497333	G -> A	LOC_Os08g20830.1	intron_variant ; MODIFIER	silent_mutation	Average:42.654; most accessible tissue: Zhenshan97 flag leaf, score: 66.327	N	N	N	N
vg0812497333	G -> DEL	N	N	silent_mutation	Average:42.654; most accessible tissue: Zhenshan97 flag leaf, score: 66.327	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0812497333	8.48E-07	NA	mr1550_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