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Detailed information for vg0631227245:

Variant ID: vg0631227245 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 31227245
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGATCAGGTGCAGTCGTTGTGGATCACCCTATGGCCAAAGTTGCAGTCGCTATAGGGACTGCACCTGATCCCGATCCCTAAAAATATGTTTTTCAGCAGC[G/A]
GCAACGCCTCGACGTGTGCACCGGCCTACTTCACCACAAGCTCATCAGGTGTAGTAGTGTGTTGCCATGATATTTAGGCTGTGTTTAGGGGGTGTTTAGA

Reverse complement sequence

TCTAAACACCCCCTAAACACAGCCTAAATATCATGGCAACACACTACTACACCTGATGAGCTTGTGGTGAAGTAGGCCGGTGCACACGTCGAGGCGTTGC[C/T]
GCTGCTGAAAAACATATTTTTAGGGATCGGGATCAGGTGCAGTCCCTATAGCGACTGCAACTTTGGCCATAGGGTGATCCACAACGACTGCACCTGATCC

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	32.20%	5.40%	0.21%	62.21%	NA
All Indica	2759	2.70%	2.00%	0.33%	95.00%	NA
All Japonica	1512	87.90%	0.10%	0.07%	11.90%	NA
Aus	269	0.40%	69.50%	0.00%	30.11%	NA
Indica I	595	3.90%	0.00%	0.50%	95.63%	NA
Indica II	465	2.60%	0.60%	0.22%	96.56%	NA
Indica III	913	1.50%	3.40%	0.00%	95.07%	NA
Indica Intermediate	786	3.30%	2.50%	0.64%	93.51%	NA
Temperate Japonica	767	93.90%	0.00%	0.13%	6.00%	NA
Tropical Japonica	504	78.20%	0.20%	0.00%	21.63%	NA
Japonica Intermediate	241	89.20%	0.40%	0.00%	10.37%	NA
VI/Aromatic	96	87.50%	6.20%	0.00%	6.25%	NA
Intermediate	90	36.70%	5.60%	0.00%	57.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0631227245	G -> A	LOC_Os06g51530.1	upstream_gene_variant ; 659.0bp to feature; MODIFIER	silent_mutation	Average:15.132; most accessible tissue: Callus, score: 85.937	N	N	N	N
vg0631227245	G -> A	LOC_Os06g51540.1	upstream_gene_variant ; 864.0bp to feature; MODIFIER	silent_mutation	Average:15.132; most accessible tissue: Callus, score: 85.937	N	N	N	N
vg0631227245	G -> A	LOC_Os06g51530-LOC_Os06g51540	intergenic_region ; MODIFIER	silent_mutation	Average:15.132; most accessible tissue: Callus, score: 85.937	N	N	N	N
vg0631227245	G -> DEL	N	N	silent_mutation	Average:15.132; most accessible tissue: Callus, score: 85.937	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0631227245	NA	3.85E-24	mr1305	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
vg0631227245	NA	8.71E-10	mr1317	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
vg0631227245	NA	6.60E-08	mr1328	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
vg0631227245	NA	6.12E-08	mr1446	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
vg0631227245	NA	9.53E-10	mr1608	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
vg0631227245	NA	1.78E-06	mr1652	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
vg0631227245	NA	4.90E-22	mr1855	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
vg0631227245	NA	2.04E-14	mr1897	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
vg0631227245	NA	2.48E-15	mr1927	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
vg0631227245	NA	7.94E-22	mr1305_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
vg0631227245	NA	1.84E-10	mr1317_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
vg0631227245	NA	3.86E-06	mr1608_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
vg0631227245	NA	1.35E-11	mr1610_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
vg0631227245	NA	1.45E-09	mr1818_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
vg0631227245	NA	1.22E-25	mr1855_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
vg0631227245	NA	1.04E-11	mr1897_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
vg0631227245	NA	1.92E-14	mr1914_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
vg0631227245	NA	1.17E-18	mr1927_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