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Detailed information for vg1119409410:

Variant ID: vg1119409410 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 19409410
Reference Allele: G	Alternative Allele: C,A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:

GCTTGCTCTAGCTTTTTGGCTGGGTGATGTTCTGTGGCGGTCACGGGCACGCGGTCGACAAGGGACTCGTGCACTACGCCAGGAGCATCGCCGACACCGC[G/C,A]
GTAGGCGAGGTGCCTCAGTGGAGCTGGGGTTCCGCGTTGTTGGCGGCTCTGTACCGTGGCCTTTGTGAGGCTTGCACGAAGACGGATCCCAGCGCGACCT

Reverse complement sequence

AGGTCGCGCTGGGATCCGTCTTCGTGCAAGCCTCACAAAGGCCACGGTACAGAGCCGCCAACAACGCGGAACCCCAGCTCCACTGAGGCACCTCGCCTAC[C/G,T]
GCGGTGTCGGCGATGCTCCTGGCGTAGTGCACGAGTCCCTTGTCGACCGCGTGCCCGTGACCGCCACAGAACATCACCCAGCCAAAAAGCTAGAGCAAGC

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	92.50%	0.80%	6.33%	0.36%	C: 0.02%
All Indica	2759	87.60%	1.30%	10.44%	0.62%	C: 0.04%
All Japonica	1512	99.70%	0.00%	0.33%	0.00%	NA
Aus	269	97.80%	1.10%	1.12%	0.00%	NA
Indica I	595	78.20%	1.50%	18.99%	1.18%	C: 0.17%
Indica II	465	94.60%	0.60%	4.73%	0.00%	NA
Indica III	913	88.70%	1.60%	9.20%	0.44%	NA
Indica Intermediate	786	89.30%	1.10%	8.78%	0.76%	NA
Temperate Japonica	767	99.70%	0.00%	0.26%	0.00%	NA
Tropical Japonica	504	99.80%	0.00%	0.20%	0.00%	NA
Japonica Intermediate	241	99.20%	0.00%	0.83%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	96.70%	0.00%	3.33%	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
vg1119409410	G -> A	LOC_Os11g32850.1	synonymous_variant ; p.Ala666Ala; LOW	synonymous_codon	Average:46.641; most accessible tissue: Minghui63 flag leaf, score: 84.973	N	N	N	N
vg1119409410	G -> DEL	LOC_Os11g32850.1	N	frameshift_variant	Average:46.641; most accessible tissue: Minghui63 flag leaf, score: 84.973	N	N	N	N
vg1119409410	G -> C	LOC_Os11g32850.1	synonymous_variant ; p.Ala666Ala; LOW	synonymous_codon	Average:46.641; most accessible tissue: Minghui63 flag leaf, score: 84.973	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1119409410	4.96E-08	4.96E-08	mr1926	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