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Detailed information for vg0321930678:

Variant ID: vg0321930678 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 21930678
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTGCCCAGAATGTCATCTGGCCATGATTCTATTTGGGTGATAGTCGACAGGCTTACAAAAGTTGCTCATTGCATCCCTGTGAGGACAACATATTCCGGAA[A/G]
TCGTTTGGCAGAATTGTATATGGCAAGGATTGTGTGTTTGCATGGTGTTCCTAAGAAAATAGTATCCGATCAAGCGAGCCAGTTTACTTCAAAGTTCTGG

Reverse complement sequence

CCAGAACTTTGAAGTAAACTGGCTCGCTTGATCGGATACTATTTTCTTAGGAACACCATGCAAACACACAATCCTTGCCATATACAATTCTGCCAAACGA[T/C]
TTCCGGAATATGTTGTCCTCACAGGGATGCAATGAGCAACTTTTGTAAGCCTGTCGACTATCACCCAAATAGAATCATGGCCAGATGACATTCTGGGCAG

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	90.90%	2.20%	3.85%	3.05%	NA
All Indica	2759	86.40%	3.10%	5.76%	4.71%	NA
All Japonica	1512	99.00%	0.10%	0.73%	0.20%	NA
Aus	269	88.50%	5.60%	3.72%	2.23%	NA
Indica I	595	89.10%	1.50%	6.22%	3.19%	NA
Indica II	465	78.10%	2.60%	6.02%	13.33%	NA
Indica III	913	89.90%	5.00%	4.05%	0.99%	NA
Indica Intermediate	786	85.20%	2.40%	7.25%	5.09%	NA
Temperate Japonica	767	99.90%	0.00%	0.13%	0.00%	NA
Tropical Japonica	504	97.40%	0.20%	1.79%	0.60%	NA
Japonica Intermediate	241	99.60%	0.00%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	91.10%	1.10%	2.22%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0321930678	A -> DEL	N	N	silent_mutation	Average:20.264; most accessible tissue: Zhenshan97 panicle, score: 32.308	N	N	N	N
vg0321930678	A -> G	LOC_Os03g39460.1	upstream_gene_variant ; 2203.0bp to feature; MODIFIER	silent_mutation	Average:20.264; most accessible tissue: Zhenshan97 panicle, score: 32.308	N	N	N	N
vg0321930678	A -> G	LOC_Os03g39490.1	upstream_gene_variant ; 3037.0bp to feature; MODIFIER	silent_mutation	Average:20.264; most accessible tissue: Zhenshan97 panicle, score: 32.308	N	N	N	N
vg0321930678	A -> G	LOC_Os03g39450.1	downstream_gene_variant ; 3721.0bp to feature; MODIFIER	silent_mutation	Average:20.264; most accessible tissue: Zhenshan97 panicle, score: 32.308	N	N	N	N
vg0321930678	A -> G	LOC_Os03g39460-LOC_Os03g39490	intergenic_region ; MODIFIER	silent_mutation	Average:20.264; most accessible tissue: Zhenshan97 panicle, score: 32.308	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0321930678	1.33E-06	9.14E-09	mr1011	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
vg0321930678	2.23E-06	2.22E-06	mr1012	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