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Detailed information for vg0608241022:

Variant ID: vg0608241022 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 8241022
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGTCACATCGGATGTTTGAACATCAATTTGAAGTATTAAAAATGTATTAATTACAAAACTAACTACGTAAATAAGAGCTAATTCACAAGACAATTTTTTT[T/A]
AAGCATAATTAATCCATACTTAGTACATGTTTACTGTAGCATCATATAGGCTAATTATGTATTAATTAGGCTCAATATATTCGTCTCGCGAATTAGTTCA

Reverse complement sequence

TGAACTAATTCGCGAGACGAATATATTGAGCCTAATTAATACATAATTAGCCTATATGATGCTACAGTAAACATGTACTAAGTATGGATTAATTATGCTT[A/T]
AAAAAAATTGTCTTGTGAATTAGCTCTTATTTACGTAGTTAGTTTTGTAATTAATACATTTTTAATACTTCAAATTGATGTTCAAACATCCGATGTGACA

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	95.40%	4.60%	0.04%	0.00%	NA
All Indica	2759	99.90%	0.10%	0.00%	0.00%	NA
All Japonica	1512	85.80%	14.10%	0.13%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	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	76.00%	23.70%	0.26%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	87.10%	12.90%	0.00%	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
vg0608241022	T -> A	LOC_Os06g14650.1	upstream_gene_variant ; 565.0bp to feature; MODIFIER	silent_mutation	Average:60.393; most accessible tissue: Minghui63 panicle, score: 79.811	N	N	N	N
vg0608241022	T -> A	LOC_Os06g14630.1	downstream_gene_variant ; 2323.0bp to feature; MODIFIER	silent_mutation	Average:60.393; most accessible tissue: Minghui63 panicle, score: 79.811	N	N	N	N
vg0608241022	T -> A	LOC_Os06g14640.1	downstream_gene_variant ; 1548.0bp to feature; MODIFIER	silent_mutation	Average:60.393; most accessible tissue: Minghui63 panicle, score: 79.811	N	N	N	N
vg0608241022	T -> A	LOC_Os06g14640-LOC_Os06g14650	intergenic_region ; MODIFIER	silent_mutation	Average:60.393; most accessible tissue: Minghui63 panicle, score: 79.811	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0608241022	9.21E-06	6.57E-06	mr1482_2	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