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Detailed information for vg1107380267:

Variant ID: vg1107380267 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 7380267
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGACTACGTCCTCCGATGGGTTCAAAGCCAAGCAGGGCGAAACAAGCTCTCACCCAAATGGGAAGGACCGTACACGATCACACAAGTTTTGCGGCCAGGC[G/A]
CATTCAAAATTGCAGACGGCGATGGTCGCGAGTTGGCAAATTCTTGGAACATTGATCAATTACGTAAATTCTATGCATAAGTCAATAGTATCCATACTTG

Reverse complement sequence

CAAGTATGGATACTATTGACTTATGCATAGAATTTACGTAATTGATCAATGTTCCAAGAATTTGCCAACTCGCGACCATCGCCGTCTGCAATTTTGAATG[C/T]
GCCTGGCCGCAAAACTTGTGTGATCGTGTACGGTCCTTCCCATTTGGGTGAGAGCTTGTTTCGCCCTGCTTGGCTTTGAACCCATCGGAGGACGTAGTCA

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	85.10%	0.80%	1.61%	12.55%	NA
All Indica	2759	77.70%	1.30%	2.50%	18.52%	NA
All Japonica	1512	94.70%	0.10%	0.33%	4.89%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	56.10%	1.50%	2.18%	40.17%	NA
Indica II	465	80.60%	0.90%	2.58%	15.91%	NA
Indica III	913	89.60%	1.20%	2.41%	6.79%	NA
Indica Intermediate	786	78.50%	1.40%	2.80%	17.30%	NA
Temperate Japonica	767	97.90%	0.00%	0.00%	2.09%	NA
Tropical Japonica	504	94.00%	0.20%	0.99%	4.76%	NA
Japonica Intermediate	241	85.90%	0.00%	0.00%	14.11%	NA
VI/Aromatic	96	99.00%	0.00%	0.00%	1.04%	NA
Intermediate	90	90.00%	0.00%	2.22%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1107380267	G -> A	LOC_Os11g13459.1	downstream_gene_variant ; 262.0bp to feature; MODIFIER	silent_mutation	Average:24.794; most accessible tissue: Minghui63 flag leaf, score: 55.781	N	N	N	N
vg1107380267	G -> A	LOC_Os11g13480.1	downstream_gene_variant ; 1599.0bp to feature; MODIFIER	silent_mutation	Average:24.794; most accessible tissue: Minghui63 flag leaf, score: 55.781	N	N	N	N
vg1107380267	G -> A	LOC_Os11g13459-LOC_Os11g13480	intergenic_region ; MODIFIER	silent_mutation	Average:24.794; most accessible tissue: Minghui63 flag leaf, score: 55.781	N	N	N	N
vg1107380267	G -> DEL	N	N	silent_mutation	Average:24.794; most accessible tissue: Minghui63 flag leaf, score: 55.781	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1107380267	4.75E-06	4.75E-06	mr1240	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