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Detailed information for vg0115994833:

Variant ID: vg0115994833 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 15994833
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTCCCTCTCATCTTAATTGTGTGTGACAAATACTTTGTGTCATGACTGGTCCTTAGCTAGATATAATTAATGCATGGAATGCTTGATTGGTTCATGAACT[G/A]
GCCTTAAATTGCAGTCAAGATCCATCCATGTGTTACAAGCAGATGTTTCGTGAATACTTTTGCTAAGCTCTGTACTGTTCTTAGCTCGAAGACTTTTGCT

Reverse complement sequence

AGCAAAAGTCTTCGAGCTAAGAACAGTACAGAGCTTAGCAAAAGTATTCACGAAACATCTGCTTGTAACACATGGATGGATCTTGACTGCAATTTAAGGC[C/T]
AGTTCATGAACCAATCAAGCATTCCATGCATTAATTATATCTAGCTAAGGACCAGTCATGACACAAAGTATTTGTCACACACAATTAAGATGAGAGGGAA

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	41.60%	0.10%	0.55%	57.72%	NA
All Indica	2759	9.10%	0.20%	0.91%	89.82%	NA
All Japonica	1512	96.20%	0.00%	0.00%	3.84%	NA
Aus	269	42.40%	0.00%	0.37%	57.25%	NA
Indica I	595	4.40%	0.20%	1.51%	93.95%	NA
Indica II	465	17.00%	0.20%	1.29%	81.51%	NA
Indica III	913	5.50%	0.00%	0.66%	93.87%	NA
Indica Intermediate	786	12.20%	0.40%	0.51%	86.90%	NA
Temperate Japonica	767	98.70%	0.00%	0.00%	1.30%	NA
Tropical Japonica	504	94.80%	0.00%	0.00%	5.16%	NA
Japonica Intermediate	241	90.90%	0.00%	0.00%	9.13%	NA
VI/Aromatic	96	95.80%	0.00%	0.00%	4.17%	NA
Intermediate	90	62.20%	0.00%	0.00%	37.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0115994833	G -> A	LOC_Os01g28570.1	upstream_gene_variant ; 3518.0bp to feature; MODIFIER	silent_mutation	Average:6.667; most accessible tissue: Zhenshan97 panicle, score: 16.188	N	N	N	N
vg0115994833	G -> A	LOC_Os01g28590.1	upstream_gene_variant ; 2690.0bp to feature; MODIFIER	silent_mutation	Average:6.667; most accessible tissue: Zhenshan97 panicle, score: 16.188	N	N	N	N
vg0115994833	G -> A	LOC_Os01g28580.1	intron_variant ; MODIFIER	silent_mutation	Average:6.667; most accessible tissue: Zhenshan97 panicle, score: 16.188	N	N	N	N
vg0115994833	G -> DEL	N	N	silent_mutation	Average:6.667; most accessible tissue: Zhenshan97 panicle, score: 16.188	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0115994833	NA	4.77E-06	mr1127_2	Ind_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
vg0115994833	NA	2.06E-06	mr1227_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
vg0115994833	NA	9.45E-07	mr1275_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
vg0115994833	NA	5.35E-06	mr1407_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