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Detailed information for vg1210741341:

Variant ID: vg1210741341 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 10741341
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.89, A: 0.12, others allele: 0.00, population size: 61. )

Flanking Sequence (100 bp) in Reference Genome:

GAGTTTGTATATTACCATGTGTTATCATTTGTAAATTTGCTTCGAATGGCAAAGGTTTGAAATAATAAAGGAAATTTCATGCATGCTATACGTACGTACC[G/A]
CCGTATATTTCATCCCTCTGGGAAGCATCCTTCTGGACAAATCGAGAGGAGTATGCCCACTATGATTTGTTAAATCTAAATTGACTTGAGGATTCCCTAA

Reverse complement sequence

TTAGGGAATCCTCAAGTCAATTTAGATTTAACAAATCATAGTGGGCATACTCCTCTCGATTTGTCCAGAAGGATGCTTCCCAGAGGGATGAAATATACGG[C/T]
GGTACGTACGTATAGCATGCATGAAATTTCCTTTATTATTTCAAACCTTTGCCATTCGAAGCAAATTTACAAATGATAACACATGGTAATATACAAACTC

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	79.90%	9.10%	0.44%	10.52%	NA
All Indica	2759	82.30%	9.40%	0.40%	7.90%	NA
All Japonica	1512	71.50%	10.40%	0.66%	17.39%	NA
Aus	269	97.00%	0.00%	0.00%	2.97%	NA
Indica I	595	88.20%	2.00%	0.17%	9.58%	NA
Indica II	465	88.80%	10.10%	0.43%	0.65%	NA
Indica III	913	79.00%	10.10%	0.44%	10.51%	NA
Indica Intermediate	786	77.70%	13.90%	0.51%	7.89%	NA
Temperate Japonica	767	79.10%	17.20%	0.39%	3.26%	NA
Tropical Japonica	504	66.90%	0.20%	0.99%	31.94%	NA
Japonica Intermediate	241	56.80%	10.40%	0.83%	31.95%	NA
VI/Aromatic	96	92.70%	7.30%	0.00%	0.00%	NA
Intermediate	90	85.60%	5.60%	0.00%	8.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1210741341	G -> DEL	N	N	silent_mutation	Average:56.931; most accessible tissue: Zhenshan97 young leaf, score: 75.039	N	N	N	N
vg1210741341	G -> A	LOC_Os12g18570.1	downstream_gene_variant ; 3117.0bp to feature; MODIFIER	silent_mutation	Average:56.931; most accessible tissue: Zhenshan97 young leaf, score: 75.039	N	N	N	N
vg1210741341	G -> A	LOC_Os12g18570-LOC_Os12g18610	intergenic_region ; MODIFIER	silent_mutation	Average:56.931; most accessible tissue: Zhenshan97 young leaf, score: 75.039	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1210741341	2.42E-06	NA	mr1882	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
vg1210741341	NA	1.65E-06	mr1164_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