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Detailed information for vg0325079496:

Variant ID: vg0325079496 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 25079496
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTCTAAGAGGGCTGGTCTGACCGTCGTGTGTTGGCCGGCCAGACCGCCGCCAGTGGGCCGGTCAGACCAGCGGTATGTGGCCCGTCTAACCGGCAGAGTC[C/T]
GAGTCAGACTCCATTTTCGTCGTTTCTCGGGTTTCCTTGCTCGGAAAGGCATGTTTCGTATTTTCATCTGTTTCTAGCCCGAGTTGGACTGGAGGAGGAC

Reverse complement sequence

GTCCTCCTCCAGTCCAACTCGGGCTAGAAACAGATGAAAATACGAAACATGCCTTTCCGAGCAAGGAAACCCGAGAAACGACGAAAATGGAGTCTGACTC[G/A]
GACTCTGCCGGTTAGACGGGCCACATACCGCTGGTCTGACCGGCCCACTGGCGGCGGTCTGGCCGGCCAACACACGACGGTCAGACCAGCCCTCTTAGAG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	98.40%	1.00%	0.68%	0.00%	NA
All Indica	2759	99.90%	0.10%	0.04%	0.00%	NA
All Japonica	1512	95.10%	2.80%	2.05%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.80%	0.00%	0.17%	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	99.70%	0.30%	0.00%	0.00%	NA
Temperate Japonica	767	95.20%	1.60%	3.26%	0.00%	NA
Tropical Japonica	504	98.80%	1.00%	0.20%	0.00%	NA
Japonica Intermediate	241	87.10%	10.80%	2.07%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	100.00%	0.00%	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
vg0325079496	C -> T	LOC_Os03g44540.1	upstream_gene_variant ; 4793.0bp to feature; MODIFIER	silent_mutation	Average:60.453; most accessible tissue: Zhenshan97 root, score: 75.275	N	N	N	N
vg0325079496	C -> T	LOC_Os03g44544.1	downstream_gene_variant ; 3598.0bp to feature; MODIFIER	silent_mutation	Average:60.453; most accessible tissue: Zhenshan97 root, score: 75.275	N	N	N	N
vg0325079496	C -> T	LOC_Os03g44550.1	downstream_gene_variant ; 2075.0bp to feature; MODIFIER	silent_mutation	Average:60.453; most accessible tissue: Zhenshan97 root, score: 75.275	N	N	N	N
vg0325079496	C -> T	LOC_Os03g44544-LOC_Os03g44550	intergenic_region ; MODIFIER	silent_mutation	Average:60.453; most accessible tissue: Zhenshan97 root, score: 75.275	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0325079496	4.54E-07	8.41E-06	mr1871	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