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Detailed information for vg1122371090:

Variant ID: vg1122371090 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 22371090
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, G: 0.01, others allele: 0.00, population size: 76. )

Flanking Sequence (100 bp) in Reference Genome:

ACGTCGAAAAAACGGCACCCCAAAATTTTGGCATTGTGTCCGGCTATTTATCTCTTTTGCACAAATTTTGGCATAAAATGGAACCTACGGTACCTTACGA[A/G]
ACCTTGGTATGGCACCACACAAACCGGCTCCAAATTCGTTCTTGTTATCCGTTTTTGGTTGTTCCCCTGTTCTCCATTATTCTGTTGAGAGCTCGGCTGG

Reverse complement sequence

CCAGCCGAGCTCTCAACAGAATAATGGAGAACAGGGGAACAACCAAAAACGGATAACAAGAACGAATTTGGAGCCGGTTTGTGTGGTGCCATACCAAGGT[T/C]
TCGTAAGGTACCGTAGGTTCCATTTTATGCCAAAATTTGTGCAAAAGAGATAAATAGCCGGACACAATGCCAAAATTTTGGGGTGCCGTTTTTTCGACGT

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	39.90%	8.80%	0.63%	50.63%	NA
All Indica	2759	26.10%	13.10%	0.43%	60.38%	NA
All Japonica	1512	63.80%	1.70%	0.60%	33.93%	NA
Aus	269	29.00%	6.70%	1.86%	62.45%	NA
Indica I	595	42.00%	11.80%	0.50%	45.71%	NA
Indica II	465	23.20%	1.50%	0.43%	74.84%	NA
Indica III	913	16.90%	24.50%	0.11%	58.49%	NA
Indica Intermediate	786	26.50%	7.60%	0.76%	65.14%	NA
Temperate Japonica	767	84.40%	2.20%	0.13%	13.30%	NA
Tropical Japonica	504	32.90%	0.80%	1.59%	64.68%	NA
Japonica Intermediate	241	62.70%	2.10%	0.00%	35.27%	NA
VI/Aromatic	96	80.20%	6.20%	1.04%	12.50%	NA
Intermediate	90	51.10%	7.80%	3.33%	37.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1122371090	A -> DEL	N	N	silent_mutation	Average:16.334; most accessible tissue: Callus, score: 46.774	N	N	N	N
vg1122371090	A -> G	LOC_Os11g37780.1	downstream_gene_variant ; 398.0bp to feature; MODIFIER	silent_mutation	Average:16.334; most accessible tissue: Callus, score: 46.774	N	N	N	N
vg1122371090	A -> G	LOC_Os11g37780-LOC_Os11g37790	intergenic_region ; MODIFIER	silent_mutation	Average:16.334; most accessible tissue: Callus, score: 46.774	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1122371090	3.76E-07	3.76E-07	mr1499	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