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Detailed information for vg1210113739:

Variant ID: vg1210113739 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 10113739
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 322. )

Flanking Sequence (100 bp) in Reference Genome:

ATATCTAATAATCTAAGCACCCTGCTTACATTATCAAATACTACTCTATACCCTCGAGAATAATATAGAGCAATCATTCGTATGAACATTAAACCCACAC[C/A]
ACTGCACCTCTCTGGTAGGCTAGTCACACAAATATATCAGCACAAATATAAATGAAAGCCAGTACTGAGACAAAGTAAAGTACTGAAAGTATATAAAGAA

Reverse complement sequence

TTCTTTATATACTTTCAGTACTTTACTTTGTCTCAGTACTGGCTTTCATTTATATTTGTGCTGATATATTTGTGTGACTAGCCTACCAGAGAGGTGCAGT[G/T]
GTGTGGGTTTAATGTTCATACGAATGATTGCTCTATATTATTCTCGAGGGTATAGAGTAGTATTTGATAATGTAAGCAGGGTGCTTAGATTATTAGATAT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	95.60%	4.00%	0.44%	0.00%	NA
All Indica	2759	99.70%	0.20%	0.04%	0.00%	NA
All Japonica	1512	87.10%	11.60%	1.32%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.70%	0.30%	0.00%	0.00%	NA
Indica II	465	99.60%	0.40%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.60%	0.30%	0.13%	0.00%	NA
Temperate Japonica	767	93.10%	5.00%	1.96%	0.00%	NA
Tropical Japonica	504	73.00%	26.00%	0.99%	0.00%	NA
Japonica Intermediate	241	97.50%	2.50%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	93.30%	6.70%	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
vg1210113739	C -> A	LOC_Os12g17650.1	downstream_gene_variant ; 4066.0bp to feature; MODIFIER	silent_mutation	Average:63.476; most accessible tissue: Minghui63 flag leaf, score: 77.494	N	N	N	N
vg1210113739	C -> A	LOC_Os12g17660.1	downstream_gene_variant ; 1813.0bp to feature; MODIFIER	silent_mutation	Average:63.476; most accessible tissue: Minghui63 flag leaf, score: 77.494	N	N	N	N
vg1210113739	C -> A	LOC_Os12g17650-LOC_Os12g17660	intergenic_region ; MODIFIER	silent_mutation	Average:63.476; most accessible tissue: Minghui63 flag leaf, score: 77.494	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1210113739	NA	6.45E-06	mr1091_2	Jap_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
vg1210113739	3.44E-07	6.07E-08	mr1110_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