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Detailed information for vg1207140697:

Variant ID: vg1207140697 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 7140697
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:

TAATTTTTATAAGACTATAAAAAATGCATGTGCGTTGCAACGGATGAAGGCTATTTTAATTTTGTTATTGTTATAAGGTTTAGTTGAAGTGAAATTGCCT[G/A]
TGGTAATTCGCTTGGATATATATTTTCTTAGAAAATCATGAGCTATAGTTAGGAGTCTGATCGTCTTAAGTTAGTATGCGAGTTTTTTAAAGAGATTTCT

Reverse complement sequence

AGAAATCTCTTTAAAAAACTCGCATACTAACTTAAGACGATCAGACTCCTAACTATAGCTCATGATTTTCTAAGAAAATATATATCCAAGCGAATTACCA[C/T]
AGGCAATTTCACTTCAACTAAACCTTATAACAATAACAAAATTAAAATAGCCTTCATCCGTTGCAACGCACATGCATTTTTTATAGTCTTATAAAAATTA

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	37.00%	8.10%	0.97%	53.91%	NA
All Indica	2759	3.80%	13.50%	1.09%	81.55%	NA
All Japonica	1512	95.30%	0.20%	0.93%	3.57%	NA
Aus	269	34.60%	0.40%	0.37%	64.68%	NA
Indica I	595	2.90%	1.00%	2.35%	93.78%	NA
Indica II	465	3.70%	44.50%	0.22%	51.61%	NA
Indica III	913	3.10%	3.90%	0.88%	92.11%	NA
Indica Intermediate	786	5.60%	15.80%	0.89%	77.74%	NA
Temperate Japonica	767	95.20%	0.30%	0.26%	4.30%	NA
Tropical Japonica	504	94.60%	0.00%	1.59%	3.77%	NA
Japonica Intermediate	241	97.10%	0.40%	1.66%	0.83%	NA
VI/Aromatic	96	47.90%	1.00%	0.00%	51.04%	NA
Intermediate	90	68.90%	6.70%	1.11%	23.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1207140697	G -> DEL	N	N	silent_mutation	Average:11.161; most accessible tissue: Callus, score: 70.559	N	N	N	N
vg1207140697	G -> A	LOC_Os12g12900.1	downstream_gene_variant ; 1770.0bp to feature; MODIFIER	silent_mutation	Average:11.161; most accessible tissue: Callus, score: 70.559	N	N	N	N
vg1207140697	G -> A	LOC_Os12g12900-LOC_Os12g12910	intergenic_region ; MODIFIER	silent_mutation	Average:11.161; most accessible tissue: Callus, score: 70.559	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1207140697	NA	5.58E-08	mr1570	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
vg1207140697	NA	9.96E-06	mr1749	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
vg1207140697	NA	7.26E-06	mr1361_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
vg1207140697	7.27E-06	7.27E-06	mr1853_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