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Detailed information for vg0432540450:

Variant ID: vg0432540450 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 32540450
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCAGCGGAAGTAATCGCCGAAGAACATTGCCCCCGGGTGGGCCAAATTCCGGAGGCCCTGAGGCGATCCACACCGCGTCATACTCCTCGCCAACTCCGAC[G/A]
TCGCCAGCATGCGGCAGACCTTTCGGGAGGGCCAGCGGGAACTTGAAGTCCCGGATGGTCCTGGCAACACGGTGTAGAACCAGTCCTTCTTCCAGTCCTC

Reverse complement sequence

GAGGACTGGAAGAAGGACTGGTTCTACACCGTGTTGCCAGGACCATCCGGGACTTCAAGTTCCCGCTGGCCCTCCCGAAAGGTCTGCCGCATGCTGGCGA[C/T]
GTCGGAGTTGGCGAGGAGTATGACGCGGTGTGGATCGCCTCAGGGCCTCCGGAATTTGGCCCACCCGGGGGCAATGTTCTTCGGCGATTACTTCCGCTGC

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	6.20%	0.20%	0.61%	93.00%	NA
All Indica	2759	0.70%	0.20%	0.98%	98.15%	NA
All Japonica	1512	15.70%	0.10%	0.07%	84.19%	NA
Aus	269	10.80%	0.70%	0.37%	88.10%	NA
Indica I	595	0.20%	0.00%	0.17%	99.66%	NA
Indica II	465	1.70%	0.40%	0.22%	97.63%	NA
Indica III	913	0.20%	0.40%	2.52%	96.82%	NA
Indica Intermediate	786	0.90%	0.00%	0.25%	98.85%	NA
Temperate Japonica	767	21.40%	0.00%	0.00%	78.62%	NA
Tropical Japonica	504	6.50%	0.20%	0.20%	93.06%	NA
Japonica Intermediate	241	16.60%	0.00%	0.00%	83.40%	NA
VI/Aromatic	96	2.10%	0.00%	0.00%	97.92%	NA
Intermediate	90	7.80%	0.00%	0.00%	92.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0432540450	G -> DEL	N	N	silent_mutation	Average:57.627; most accessible tissue: Zhenshan97 panicle, score: 82.888	N	N	N	N
vg0432540450	G -> A	LOC_Os04g54680.1	downstream_gene_variant ; 3252.0bp to feature; MODIFIER	silent_mutation	Average:57.627; most accessible tissue: Zhenshan97 panicle, score: 82.888	N	N	N	N
vg0432540450	G -> A	LOC_Os04g54710.1	intron_variant ; MODIFIER	silent_mutation	Average:57.627; most accessible tissue: Zhenshan97 panicle, score: 82.888	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0432540450	4.74E-07	NA	mr1406	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
vg0432540450	1.54E-06	1.54E-06	mr1406	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
vg0432540450	2.39E-06	NA	mr1406_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
vg0432540450	8.25E-06	8.25E-06	mr1406_2	Jap_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