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Detailed information for vg0224598014:

Variant ID: vg0224598014 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 24598014
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAGATCGATACGACTTGGTCAGTTTTATGCGGAGTTTCGTGAACGTTTGATCACTCGGGAACGGGCGACGTCGTACGATTTCTATACGGTCCAGAATTCC[T/A]
GATCTCCTGATTCCTATACACCCGAAGACCCGCAGTCCAAGGATTTCGAGGATCAAGCTCAAGATCTCGAGCAAGGCAAGCCACCTTTGAACATCTTGAG

Reverse complement sequence

CTCAAGATGTTCAAAGGTGGCTTGCCTTGCTCGAGATCTTGAGCTTGATCCTCGAAATCCTTGGACTGCGGGTCTTCGGGTGTATAGGAATCAGGAGATC[A/T]
GGAATTCTGGACCGTATAGAAATCGTACGACGTCGCCCGTTCCCGAGTGATCAAACGTTCACGAAACTCCGCATAAAACTGACCAAGTCGTATCGATCTT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	91.20%	8.70%	0.04%	0.00%	NA
All Indica	2759	96.70%	3.30%	0.00%	0.00%	NA
All Japonica	1512	81.40%	18.50%	0.13%	0.00%	NA
Aus	269	93.70%	6.30%	0.00%	0.00%	NA
Indica I	595	98.30%	1.70%	0.00%	0.00%	NA
Indica II	465	98.50%	1.50%	0.00%	0.00%	NA
Indica III	913	95.70%	4.30%	0.00%	0.00%	NA
Indica Intermediate	786	95.70%	4.30%	0.00%	0.00%	NA
Temperate Japonica	767	81.90%	18.00%	0.13%	0.00%	NA
Tropical Japonica	504	83.50%	16.50%	0.00%	0.00%	NA
Japonica Intermediate	241	75.50%	24.10%	0.41%	0.00%	NA
VI/Aromatic	96	81.20%	18.80%	0.00%	0.00%	NA
Intermediate	90	91.10%	8.90%	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
vg0224598014	T -> A	LOC_Os02g40540.1	upstream_gene_variant ; 4537.0bp to feature; MODIFIER	silent_mutation	Average:49.219; most accessible tissue: Callus, score: 74.654	N	N	N	N
vg0224598014	T -> A	LOC_Os02g40560.1	upstream_gene_variant ; 128.0bp to feature; MODIFIER	silent_mutation	Average:49.219; most accessible tissue: Callus, score: 74.654	N	N	N	N
vg0224598014	T -> A	LOC_Os02g40570.1	upstream_gene_variant ; 1758.0bp to feature; MODIFIER	silent_mutation	Average:49.219; most accessible tissue: Callus, score: 74.654	N	N	N	N
vg0224598014	T -> A	LOC_Os02g40550.1	downstream_gene_variant ; 1046.0bp to feature; MODIFIER	silent_mutation	Average:49.219; most accessible tissue: Callus, score: 74.654	N	N	N	N
vg0224598014	T -> A	LOC_Os02g40560-LOC_Os02g40570	intergenic_region ; MODIFIER	silent_mutation	Average:49.219; most accessible tissue: Callus, score: 74.654	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0224598014	2.24E-06	NA	mr1672	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