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Detailed information for vg0417132051:

Variant ID: vg0417132051 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 17132051
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCGTATCACACTACTACAGAAAACACATACAGTTCAATACTATATGTGCCGGAACAGTTAAAACCAATAACTACAGATCTCTTCCCACCTTTGCATGGTG[A/G]
AAAAAATAAAATAAAATCGACACCTTTTACCAACTATAGGTGTTAGTTCTAAAGAAAAACCAGCACCAACACTTTTAAGTCCCATTTTTTTAACAAAACG

Reverse complement sequence

CGTTTTGTTAAAAAAATGGGACTTAAAAGTGTTGGTGCTGGTTTTTCTTTAGAACTAACACCTATAGTTGGTAAAAGGTGTCGATTTTATTTTATTTTTT[T/C]
CACCATGCAAAGGTGGGAAGAGATCTGTAGTTATTGGTTTTAACTGTTCCGGCACATATAGTATTGAACTGTATGTGTTTTCTGTAGTAGTGTGATACGC

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	85.70%	9.50%	3.58%	1.21%	NA
All Indica	2759	96.00%	1.10%	2.46%	0.36%	NA
All Japonica	1512	66.50%	27.10%	6.08%	0.33%	NA
Aus	269	96.30%	0.00%	0.74%	2.97%	NA
Indica I	595	94.60%	0.20%	5.21%	0.00%	NA
Indica II	465	95.50%	2.60%	1.51%	0.43%	NA
Indica III	913	98.00%	1.00%	0.44%	0.55%	NA
Indica Intermediate	786	95.20%	1.10%	3.31%	0.38%	NA
Temperate Japonica	767	64.80%	26.90%	7.95%	0.39%	NA
Tropical Japonica	504	59.50%	36.30%	3.97%	0.20%	NA
Japonica Intermediate	241	86.70%	8.30%	4.56%	0.41%	NA
VI/Aromatic	96	65.60%	0.00%	0.00%	34.38%	NA
Intermediate	90	78.90%	12.20%	7.78%	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
vg0417132051	A -> DEL	N	N	silent_mutation	Average:60.719; most accessible tissue: Callus, score: 90.106	N	N	N	N
vg0417132051	A -> G	LOC_Os04g28900.1	upstream_gene_variant ; 3723.0bp to feature; MODIFIER	silent_mutation	Average:60.719; most accessible tissue: Callus, score: 90.106	N	N	N	N
vg0417132051	A -> G	LOC_Os04g28910.1	upstream_gene_variant ; 4853.0bp to feature; MODIFIER	silent_mutation	Average:60.719; most accessible tissue: Callus, score: 90.106	N	N	N	N
vg0417132051	A -> G	LOC_Os04g28900-LOC_Os04g28910	intergenic_region ; MODIFIER	silent_mutation	Average:60.719; most accessible tissue: Callus, score: 90.106	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0417132051	1.74E-08	NA	mr1301	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
vg0417132051	5.30E-07	NA	mr1410	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
vg0417132051	NA	6.25E-06	mr1296_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
vg0417132051	3.60E-10	NA	mr1301_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
vg0417132051	9.45E-07	NA	mr1301_2	Jap_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
vg0417132051	1.09E-06	NA	mr1410_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
vg0417132051	NA	1.30E-07	mr1749_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
vg0417132051	NA	7.58E-08	mr1821_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