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Detailed information for vg0915069345:

Variant ID: vg0915069345 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 15069345
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGTTAATTTTGGGGTTTTTTCATCGAAGTTTATTTTTCAGCTTTTGTTTTTAGATCGCTTAGAACACGTATATAAAAGTTTTATTCACAAATTATTTTTC[G/A]
TTTGCAAATATGCCGTTTCGCTTATTCCCCGAATAAGCGAAACGATGGGTCGCATAGTAGATGTTTTTGTAGCTCGAAACCAGATGTGCCAAAGATTAGA

Reverse complement sequence

TCTAATCTTTGGCACATCTGGTTTCGAGCTACAAAAACATCTACTATGCGACCCATCGTTTCGCTTATTCGGGGAATAAGCGAAACGGCATATTTGCAAA[C/T]
GAAAAATAATTTGTGAATAAAACTTTTATATACGTGTTCTAAGCGATCTAAAAACAAAAGCTGAAAAATAAACTTCGATGAAAAAACCCCAAAATTAACT

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	78.00%	21.60%	0.32%	0.11%	NA
All Indica	2759	99.60%	0.40%	0.04%	0.04%	NA
All Japonica	1512	40.30%	58.90%	0.73%	0.00%	NA
Aus	269	97.80%	1.50%	0.00%	0.74%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	99.10%	0.60%	0.00%	0.22%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	99.20%	0.60%	0.13%	0.00%	NA
Temperate Japonica	767	67.00%	32.30%	0.65%	0.00%	NA
Tropical Japonica	504	5.40%	93.70%	0.99%	0.00%	NA
Japonica Intermediate	241	28.60%	71.00%	0.41%	0.00%	NA
VI/Aromatic	96	12.50%	84.40%	1.04%	2.08%	NA
Intermediate	90	60.00%	37.80%	2.22%	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
vg0915069345	G -> DEL	N	N	silent_mutation	Average:29.83; most accessible tissue: Zhenshan97 panicle, score: 49.416	N	N	N	N
vg0915069345	G -> A	LOC_Os09g25130-LOC_Os09g25150	intergenic_region ; MODIFIER	silent_mutation	Average:29.83; most accessible tissue: Zhenshan97 panicle, score: 49.416	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0915069345	NA	5.60E-06	mr1211	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
vg0915069345	NA	1.21E-06	mr1527	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
vg0915069345	NA	1.01E-09	mr1646_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