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Detailed information for vg0332988748:

Variant ID: vg0332988748 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 32988748
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GATAATACTTGTCGTTTTGCTAACAATTTTATACATATTATAATTTAAAATAATGGTCAAAGTTGTTTTTTGGAGACCGTGCCCTTATACAAAAGGGCAA[G/A]
TATTATCAACCCGGAGGGAGTACAATTCTACAACCTTTTTCTTTTTTTTTTTGGCGTGGAACATATAACTGAATACAACTCTACGTATAGTTGGACTAAC

Reverse complement sequence

GTTAGTCCAACTATACGTAGAGTTGTATTCAGTTATATGTTCCACGCCAAAAAAAAAAAGAAAAAGGTTGTAGAATTGTACTCCCTCCGGGTTGATAATA[C/T]
TTGCCCTTTTGTATAAGGGCACGGTCTCCAAAAAACAACTTTGACCATTATTTTAAATTATAATATGTATAAAATTGTTAGCAAAACGACAAGTATTATC

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	92.40%	5.30%	2.35%	0.00%	NA
All Indica	2759	99.30%	0.20%	0.51%	0.00%	NA
All Japonica	1512	77.60%	16.00%	6.42%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.50%	0.00%	0.50%	0.00%	NA
Indica II	465	98.50%	1.10%	0.43%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	98.70%	0.10%	1.15%	0.00%	NA
Temperate Japonica	767	65.80%	24.40%	9.78%	0.00%	NA
Tropical Japonica	504	94.40%	4.00%	1.59%	0.00%	NA
Japonica Intermediate	241	79.70%	14.50%	5.81%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0332988748	G -> A	LOC_Os03g57910.1	upstream_gene_variant ; 2582.0bp to feature; MODIFIER	silent_mutation	Average:43.959; most accessible tissue: Callus, score: 67.277	N	N	N	N
vg0332988748	G -> A	LOC_Os03g57920.1	upstream_gene_variant ; 630.0bp to feature; MODIFIER	silent_mutation	Average:43.959; most accessible tissue: Callus, score: 67.277	N	N	N	N
vg0332988748	G -> A	LOC_Os03g57930.1	downstream_gene_variant ; 286.0bp to feature; MODIFIER	silent_mutation	Average:43.959; most accessible tissue: Callus, score: 67.277	N	N	N	N
vg0332988748	G -> A	LOC_Os03g57920-LOC_Os03g57930	intergenic_region ; MODIFIER	silent_mutation	Average:43.959; most accessible tissue: Callus, score: 67.277	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0332988748	9.34E-07	NA	mr1174_2	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