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Detailed information for vg0129297761:

Variant ID: vg0129297761 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 29297761
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCACAGCCAATCAGAATAACAAAACTGAATGGTTTCATCCAGCCAAATCGACCGGATGCACTCATCCAGTATATTGAGAGAATATTCCCTATTCTGGGCC[G/A]
TCCCATCCACCCTGCCCTCCAACCAAACCGCACGAAAACTCGTGCGGCCATCTCATCCATCCAACCAAACACATCTTAAGTGATCCAATTTGGTAGGTTG

Reverse complement sequence

CAACCTACCAAATTGGATCACTTAAGATGTGTTTGGTTGGATGGATGAGATGGCCGCACGAGTTTTCGTGCGGTTTGGTTGGAGGGCAGGGTGGATGGGA[C/T]
GGCCCAGAATAGGGAATATTCTCTCAATATACTGGATGAGTGCATCCGGTCGATTTGGCTGGATGAAACCATTCAGTTTTGTTATTCTGATTGGCTGTGG

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%	7.60%	0.02%	0.00%	NA
All Indica	2759	92.30%	7.70%	0.00%	0.00%	NA
All Japonica	1512	99.80%	0.20%	0.00%	0.00%	NA
Aus	269	51.30%	48.30%	0.37%	0.00%	NA
Indica I	595	97.60%	2.40%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	85.90%	14.10%	0.00%	0.00%	NA
Indica Intermediate	786	91.30%	8.70%	0.00%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	90.60%	9.40%	0.00%	0.00%	NA
Intermediate	90	93.30%	6.70%	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
vg0129297761	G -> A	LOC_Os01g50990.1	upstream_gene_variant ; 280.0bp to feature; MODIFIER	silent_mutation	Average:56.162; most accessible tissue: Callus, score: 80.438	N	N	N	N
vg0129297761	G -> A	LOC_Os01g51000.1	upstream_gene_variant ; 3499.0bp to feature; MODIFIER	silent_mutation	Average:56.162; most accessible tissue: Callus, score: 80.438	N	N	N	N
vg0129297761	G -> A	LOC_Os01g50980.1	downstream_gene_variant ; 2319.0bp to feature; MODIFIER	silent_mutation	Average:56.162; most accessible tissue: Callus, score: 80.438	N	N	N	N
vg0129297761	G -> A	LOC_Os01g50980-LOC_Os01g50990	intergenic_region ; MODIFIER	silent_mutation	Average:56.162; most accessible tissue: Callus, score: 80.438	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0129297761	4.97E-06	1.36E-09	mr1511_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