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Detailed information for vg1209428340:

Variant ID: vg1209428340 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 9428340
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, G: 0.00, others allele: 0.00, population size: 281. )

Flanking Sequence (100 bp) in Reference Genome:

GGTGGAGAGAAAAAAAAGGATGTGCATGGTCCGTGCTAGTGGCGGAGAGAAAAAAAATTGCGCGCAAATAGGATTTGAGATCTGGAGACAAAGTAGACTT[A/G]
TTCCGAGTAATAATAAGTGTAAAAGTTTTAGATAGGGTAGGTCAATCTGGCCTAGGAGAGGCCCATAGACAGTGCGAGTAATAATACGAAACTCCTAATT

Reverse complement sequence

AATTAGGAGTTTCGTATTATTACTCGCACTGTCTATGGGCCTCTCCTAGGCCAGATTGACCTACCCTATCTAAAACTTTTACACTTATTATTACTCGGAA[T/C]
AAGTCTACTTTGTCTCCAGATCTCAAATCCTATTTGCGCGCAATTTTTTTTCTCTCCGCCACTAGCACGGACCATGCACATCCTTTTTTTTCTCTCCACC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	79.80%	15.20%	1.27%	3.75%	NA
All Indica	2759	68.60%	24.80%	1.63%	4.97%	NA
All Japonica	1512	99.00%	0.90%	0.07%	0.07%	NA
Aus	269	81.80%	0.40%	4.09%	13.75%	NA
Indica I	595	85.90%	11.90%	1.85%	0.34%	NA
Indica II	465	78.30%	17.60%	1.29%	2.80%	NA
Indica III	913	52.20%	35.00%	1.86%	10.84%	NA
Indica Intermediate	786	69.00%	26.70%	1.40%	2.93%	NA
Temperate Japonica	767	99.90%	0.00%	0.13%	0.00%	NA
Tropical Japonica	504	97.20%	2.60%	0.00%	0.20%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	84.40%	13.50%	1.04%	1.04%	NA
Intermediate	90	88.90%	7.80%	2.22%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1209428340	A -> DEL	N	N	silent_mutation	Average:60.073; most accessible tissue: Minghui63 root, score: 72.134	N	N	N	N
vg1209428340	A -> G	LOC_Os12g16460.1	upstream_gene_variant ; 2453.0bp to feature; MODIFIER	silent_mutation	Average:60.073; most accessible tissue: Minghui63 root, score: 72.134	N	N	N	N
vg1209428340	A -> G	LOC_Os12g16450.1	downstream_gene_variant ; 4740.0bp to feature; MODIFIER	silent_mutation	Average:60.073; most accessible tissue: Minghui63 root, score: 72.134	N	N	N	N
vg1209428340	A -> G	LOC_Os12g16460-LOC_Os12g16470	intergenic_region ; MODIFIER	silent_mutation	Average:60.073; most accessible tissue: Minghui63 root, score: 72.134	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1209428340	NA	1.75E-06	mr1200	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
vg1209428340	2.09E-06	2.09E-06	mr1449	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