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Detailed information for vg0711326131:

Variant ID: vg0711326131 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 11326131
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CACAACCCATCCTTTACAAGCATTTCCCCTTATTTCATTGCAGCTTACATTTATCAAACATATGGCCAGTTTGCCGCTATGGAATGTTCAGAAATTACAA[G/A]
TAAAGGAGGCCGAAAGCCATTCCTAGTCCGAAATTTATTGTTGGTACATTAAGTTATTCATTCTACATACATTTTTATTCAATAAACGCATATAAAACCA

Reverse complement sequence

TGGTTTTATATGCGTTTATTGAATAAAAATGTATGTAGAATGAATAACTTAATGTACCAACAATAAATTTCGGACTAGGAATGGCTTTCGGCCTCCTTTA[C/T]
TTGTAATTTCTGAACATTCCATAGCGGCAAACTGGCCATATGTTTGATAAATGTAAGCTGCAATGAAATAAGGGGAAATGCTTGTAAAGGATGGGTTGTG

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	96.00%	1.10%	1.35%	1.52%	NA
All Indica	2759	99.90%	0.00%	0.11%	0.00%	NA
All Japonica	1512	88.60%	3.40%	3.97%	4.10%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.60%	0.00%	0.38%	0.00%	NA
Temperate Japonica	767	89.60%	3.30%	7.17%	0.00%	NA
Tropical Japonica	504	87.30%	0.20%	0.60%	11.90%	NA
Japonica Intermediate	241	88.00%	10.40%	0.83%	0.83%	NA
VI/Aromatic	96	92.70%	0.00%	1.04%	6.25%	NA
Intermediate	90	95.60%	0.00%	0.00%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0711326131	G -> DEL	N	N	silent_mutation	Average:36.206; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N
vg0711326131	G -> A	LOC_Os07g19120.1	upstream_gene_variant ; 3134.0bp to feature; MODIFIER	silent_mutation	Average:36.206; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N
vg0711326131	G -> A	LOC_Os07g19140.1	upstream_gene_variant ; 3519.0bp to feature; MODIFIER	silent_mutation	Average:36.206; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N
vg0711326131	G -> A	LOC_Os07g19130.1	downstream_gene_variant ; 207.0bp to feature; MODIFIER	silent_mutation	Average:36.206; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N
vg0711326131	G -> A	LOC_Os07g19120-LOC_Os07g19130	intergenic_region ; MODIFIER	silent_mutation	Average:36.206; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0711326131	7.37E-07	9.80E-08	mr1842_2	Jap_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