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Detailed information for vg0713260653:

Variant ID: vg0713260653 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 13260653
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCCGGCGATCACCTACGGGGTGGCGGCGGCCTTCCGGTCGCCACCTACTCTGTCCCGGAACAGCAATACGAATCCCTTCCAGCGCAACTGAGAATCGGGA[A/G]
ATTAGGGTTTTGGGATGTCGGGGAGATTGGAACCGTGAGTGAGATCGTCATCTTTCTCACGGGCCGGCCTCCCCTTTTATTTTTTGCGCTGAGGGAATCG

Reverse complement sequence

CGATTCCCTCAGCGCAAAAAATAAAAGGGGAGGCCGGCCCGTGAGAAAGATGACGATCTCACTCACGGTTCCAATCTCCCCGACATCCCAAAACCCTAAT[T/C]
TCCCGATTCTCAGTTGCGCTGGAAGGGATTCGTATTGCTGTTCCGGGACAGAGTAGGTGGCGACCGGAAGGCCGCCGCCACCCCGTAGGTGATCGCCGGC

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	39.70%	22.30%	5.59%	32.48%	NA
All Indica	2759	61.00%	2.00%	2.03%	34.94%	NA
All Japonica	1512	6.30%	62.90%	6.15%	24.67%	NA
Aus	269	26.00%	5.60%	18.96%	49.44%	NA
Indica I	595	28.40%	1.50%	3.03%	67.06%	NA
Indica II	465	35.70%	4.50%	2.37%	57.42%	NA
Indica III	913	92.70%	0.00%	1.75%	5.59%	NA
Indica Intermediate	786	64.00%	3.20%	1.40%	31.42%	NA
Temperate Japonica	767	5.90%	63.40%	2.74%	28.03%	NA
Tropical Japonica	504	2.00%	74.80%	12.70%	10.52%	NA
Japonica Intermediate	241	16.60%	36.50%	3.32%	43.57%	NA
VI/Aromatic	96	1.00%	5.20%	51.04%	42.71%	NA
Intermediate	90	26.70%	30.00%	16.67%	26.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0713260653	A -> DEL	N	N	silent_mutation	Average:8.719; most accessible tissue: Callus, score: 15.682	N	N	N	N
vg0713260653	A -> G	LOC_Os07g23470.1	upstream_gene_variant ; 1983.0bp to feature; MODIFIER	silent_mutation	Average:8.719; most accessible tissue: Callus, score: 15.682	N	N	N	N
vg0713260653	A -> G	LOC_Os07g23480.1	downstream_gene_variant ; 465.0bp to feature; MODIFIER	silent_mutation	Average:8.719; most accessible tissue: Callus, score: 15.682	N	N	N	N
vg0713260653	A -> G	LOC_Os07g23470-LOC_Os07g23480	intergenic_region ; MODIFIER	silent_mutation	Average:8.719; most accessible tissue: Callus, score: 15.682	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0713260653	3.06E-08	1.51E-26	mr1133	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
vg0713260653	1.08E-07	1.07E-18	mr1133	Ind_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
vg0713260653	NA	4.04E-06	mr1533	Ind_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
vg0713260653	NA	1.58E-06	mr1662	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
vg0713260653	NA	9.59E-08	mr1662	Ind_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
vg0713260653	1.05E-07	1.89E-16	mr1667	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
vg0713260653	2.81E-08	2.17E-14	mr1667	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
vg0713260653	NA	2.47E-07	mr1980	Ind_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
vg0713260653	8.42E-08	1.41E-25	mr1133_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
vg0713260653	5.14E-06	1.07E-15	mr1133_2	Ind_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
vg0713260653	NA	3.71E-07	mr1662_2	Ind_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
vg0713260653	4.54E-07	2.68E-16	mr1667_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
vg0713260653	2.75E-06	8.02E-12	mr1667_2	Ind_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