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Detailed information for vg0817776989:

Variant ID: vg0817776989 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 17776989
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAAAACCATCTAATATCAATTTCCTCTTGAGTCAAAAGGACATTTTCCGCCTTTTATCTAGCAAATTTAACTTATCCAATAAATCTTTTTTCTCTTTTTT[A/G]
TATATACCACTCGTGTGCTTAGCCCATCCCCTCAAGTGTTGCCTTAAACGACGTATTTTTGCTTGCCAGCGCTCAATAGGAGAGTCTCCTTCATCCACAC

Reverse complement sequence

GTGTGGATGAAGGAGACTCTCCTATTGAGCGCTGGCAAGCAAAAATACGTCGTTTAAGGCAACACTTGAGGGGATGGGCTAAGCACACGAGTGGTATATA[T/C]
AAAAAAGAGAAAAAAGATTTATTGGATAAGTTAAATTTGCTAGATAAAAGGCGGAAAATGTCCTTTTGACTCAAGAGGAAATTGATATTAGATGGTTTTA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	92.50%	1.70%	0.44%	5.40%	NA
All Indica	2759	99.90%	0.00%	0.07%	0.00%	NA
All Japonica	1512	77.20%	5.10%	0.86%	16.80%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.00%	0.22%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.90%	0.00%	0.13%	0.00%	NA
Temperate Japonica	767	93.40%	2.70%	0.52%	3.39%	NA
Tropical Japonica	504	57.90%	2.40%	0.99%	38.69%	NA
Japonica Intermediate	241	66.40%	18.30%	1.66%	13.69%	NA
VI/Aromatic	96	92.70%	1.00%	6.25%	0.00%	NA
Intermediate	90	98.90%	0.00%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0817776989	A -> G	LOC_Os08g29040.1	upstream_gene_variant ; 4292.0bp to feature; MODIFIER	silent_mutation	Average:20.837; most accessible tissue: Minghui63 young leaf, score: 32.638	N	N	N	N
vg0817776989	A -> G	LOC_Os08g29030.1	intron_variant ; MODIFIER	silent_mutation	Average:20.837; most accessible tissue: Minghui63 young leaf, score: 32.638	N	N	N	N
vg0817776989	A -> DEL	N	N	silent_mutation	Average:20.837; most accessible tissue: Minghui63 young leaf, score: 32.638	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0817776989	2.31E-06	2.31E-06	mr1542_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