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Detailed information for vg1120997358:

Variant ID: vg1120997358 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 20997358
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, others allele: 0.00, population size: 218. )

Flanking Sequence (100 bp) in Reference Genome:

CGTGCAACACAGAGTGAGTTTTTATTGTCATTCGAACAAATTTCATTCCCATATATATAACATGTACATTCTGATATTTATCTCATCTCACGCATATTCC[A/G]
GATTCCACTGGGTCCTATTATTTTTCGACTTGGACGCATGCAGAGTCACTGTGTACGACTCAATGAATAAAGAGGAGAAGGTTTTTGACAAGGTCTTCCA

Reverse complement sequence

TGGAAGACCTTGTCAAAAACCTTCTCCTCTTTATTCATTGAGTCGTACACAGTGACTCTGCATGCGTCCAAGTCGAAAAATAATAGGACCCAGTGGAATC[T/C]
GGAATATGCGTGAGATGAGATAAATATCAGAATGTACATGTTATATATATGGGAATGAAATTTGTTCGAATGACAATAAAAACTCACTCTGTGTTGCACG

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	72.00%	21.10%	4.93%	1.93%	NA
All Indica	2759	54.30%	34.80%	7.97%	3.01%	NA
All Japonica	1512	98.10%	0.90%	0.46%	0.53%	NA
Aus	269	95.50%	3.70%	0.74%	0.00%	NA
Indica I	595	81.30%	11.10%	4.87%	2.69%	NA
Indica II	465	54.80%	28.60%	10.97%	5.59%	NA
Indica III	913	40.60%	52.20%	6.02%	1.10%	NA
Indica Intermediate	786	49.20%	36.00%	10.81%	3.94%	NA
Temperate Japonica	767	97.80%	0.40%	0.91%	0.91%	NA
Tropical Japonica	504	97.80%	2.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.00%	0.00%	0.41%	NA
VI/Aromatic	96	96.90%	3.10%	0.00%	0.00%	NA
Intermediate	90	81.10%	14.40%	4.44%	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
vg1120997358	A -> DEL	N	N	silent_mutation	Average:17.498; most accessible tissue: Zhenshan97 flower, score: 26.922	N	N	N	N
vg1120997358	A -> G	LOC_Os11g35770.1	downstream_gene_variant ; 2035.0bp to feature; MODIFIER	silent_mutation	Average:17.498; most accessible tissue: Zhenshan97 flower, score: 26.922	N	N	N	N
vg1120997358	A -> G	LOC_Os11g35762.1	intron_variant ; MODIFIER	silent_mutation	Average:17.498; most accessible tissue: Zhenshan97 flower, score: 26.922	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1120997358	NA	6.93E-07	mr1363_2	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
vg1120997358	3.91E-06	NA	mr1803_2	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