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Detailed information for vg0805288335:

Variant ID: vg0805288335 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 5288335
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGCCTATCTCATGTATAAATAGAGGGGGAGCGTGAGGCTTTCCGGTATCGCTTTAGAGAGCAATTGAGTTGAGTTTTGAGTTAGGGTTTCGAGTTTAGTC[G/A]
AAATTTTTGTAAGGAGTACTGTTGTTGCACTTTGTAAACACAAAGAGAAGTAATAAAGTCGTCATCCACTTTAAGAGTTCTTCGATTTGTGTTTTACCGG

Reverse complement sequence

CCGGTAAAACACAAATCGAAGAACTCTTAAAGTGGATGACGACTTTATTACTTCTCTTTGTGTTTACAAAGTGCAACAACAGTACTCCTTACAAAAATTT[C/T]
GACTAAACTCGAAACCCTAACTCAAAACTCAACTCAATTGCTCTCTAAAGCGATACCGGAAAGCCTCACGCTCCCCCTCTATTTATACATGAGATAGGCA

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	78.50%	12.50%	0.32%	8.65%	NA
All Indica	2759	81.80%	13.60%	0.18%	4.49%	NA
All Japonica	1512	80.40%	0.30%	0.66%	18.72%	NA
Aus	269	56.10%	43.90%	0.00%	0.00%	NA
Indica I	595	98.70%	1.30%	0.00%	0.00%	NA
Indica II	465	67.10%	10.10%	0.43%	22.37%	NA
Indica III	913	81.50%	18.40%	0.11%	0.00%	NA
Indica Intermediate	786	78.00%	19.20%	0.25%	2.54%	NA
Temperate Japonica	767	72.10%	0.00%	0.65%	27.25%	NA
Tropical Japonica	504	97.00%	0.40%	0.40%	2.18%	NA
Japonica Intermediate	241	71.80%	0.80%	1.24%	26.14%	NA
VI/Aromatic	96	14.60%	85.40%	0.00%	0.00%	NA
Intermediate	90	83.30%	14.40%	0.00%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0805288335	G -> A	LOC_Os08g09130.1	downstream_gene_variant ; 2733.0bp to feature; MODIFIER	silent_mutation	Average:28.054; most accessible tissue: Zhenshan97 root, score: 71.691	N	N	N	N
vg0805288335	G -> A	LOC_Os08g09130-LOC_Os08g09140	intergenic_region ; MODIFIER	silent_mutation	Average:28.054; most accessible tissue: Zhenshan97 root, score: 71.691	N	N	N	N
vg0805288335	G -> DEL	N	N	silent_mutation	Average:28.054; most accessible tissue: Zhenshan97 root, score: 71.691	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0805288335	4.89E-06	NA	mr1167_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
vg0805288335	7.77E-06	NA	mr1950_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251