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Detailed information for vg0715290134:

Variant ID: vg0715290134 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 15290134
Reference Allele: G	Alternative Allele: A,T
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGCAATTTCCCCCCTAACTGTGCAATTAGTTTTTTAATTTATCTCTATTTAATACTTCATACATGTGTCTAAAGATTCGATGTGATGTTTTTTGGAAAAA[G/A,T]
TTTTTGGGAACTAAACAGGGCCTTAGATAAGTTAGAGTAAAAAAACCAAAGAACCTTAGAGGGCATTAGAGAAGAAAATGAAGTGCCAAATACACTGCGC

Reverse complement sequence

GCGCAGTGTATTTGGCACTTCATTTTCTTCTCTAATGCCCTCTAAGGTTCTTTGGTTTTTTTACTCTAACTTATCTAAGGCCCTGTTTAGTTCCCAAAAA[C/T,A]
TTTTTCCAAAAAACATCACATCGAATCTTTAGACACATGTATGAAGTATTAAATAGAGATAAATTAAAAAACTAATTGCACAGTTAGGGGGGAAATTGCG

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	43.90%	43.10%	3.70%	9.33%	T: 0.02%
All Indica	2759	18.10%	64.40%	5.98%	11.45%	T: 0.04%
All Japonica	1512	93.50%	0.70%	0.40%	5.36%	NA
Aus	269	20.10%	75.10%	0.37%	4.46%	NA
Indica I	595	9.20%	75.10%	7.56%	8.07%	NA
Indica II	465	6.90%	73.30%	8.82%	10.97%	NA
Indica III	913	20.30%	63.40%	2.30%	14.02%	NA
Indica Intermediate	786	28.90%	52.30%	7.38%	11.32%	T: 0.13%
Temperate Japonica	767	88.10%	0.90%	0.65%	10.30%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	97.90%	0.80%	0.41%	0.83%	NA
VI/Aromatic	96	56.20%	12.50%	1.04%	30.21%	NA
Intermediate	90	58.90%	35.60%	2.22%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0715290134	G -> DEL	N	N	silent_mutation	Average:61.691; most accessible tissue: Zhenshan97 flower, score: 84.783	N	N	N	N
vg0715290134	G -> A	LOC_Os07g26540.1	upstream_gene_variant ; 3022.0bp to feature; MODIFIER	silent_mutation	Average:61.691; most accessible tissue: Zhenshan97 flower, score: 84.783	N	N	N	N
vg0715290134	G -> A	LOC_Os07g26530.1	downstream_gene_variant ; 4948.0bp to feature; MODIFIER	silent_mutation	Average:61.691; most accessible tissue: Zhenshan97 flower, score: 84.783	N	N	N	N
vg0715290134	G -> A	LOC_Os07g26550.1	downstream_gene_variant ; 4755.0bp to feature; MODIFIER	silent_mutation	Average:61.691; most accessible tissue: Zhenshan97 flower, score: 84.783	N	N	N	N
vg0715290134	G -> A	LOC_Os07g26530-LOC_Os07g26540	intergenic_region ; MODIFIER	silent_mutation	Average:61.691; most accessible tissue: Zhenshan97 flower, score: 84.783	N	N	N	N
vg0715290134	G -> T	LOC_Os07g26540.1	upstream_gene_variant ; 3022.0bp to feature; MODIFIER	silent_mutation	Average:61.691; most accessible tissue: Zhenshan97 flower, score: 84.783	N	N	N	N
vg0715290134	G -> T	LOC_Os07g26530.1	downstream_gene_variant ; 4948.0bp to feature; MODIFIER	silent_mutation	Average:61.691; most accessible tissue: Zhenshan97 flower, score: 84.783	N	N	N	N
vg0715290134	G -> T	LOC_Os07g26550.1	downstream_gene_variant ; 4755.0bp to feature; MODIFIER	silent_mutation	Average:61.691; most accessible tissue: Zhenshan97 flower, score: 84.783	N	N	N	N
vg0715290134	G -> T	LOC_Os07g26530-LOC_Os07g26540	intergenic_region ; MODIFIER	silent_mutation	Average:61.691; most accessible tissue: Zhenshan97 flower, score: 84.783	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0715290134	NA	1.14E-11	mr1281	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
vg0715290134	NA	3.88E-06	mr1291	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
vg0715290134	4.84E-06	4.41E-07	mr1510	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
vg0715290134	NA	1.89E-24	mr1537	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
vg0715290134	NA	2.02E-18	mr1566	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
vg0715290134	NA	3.32E-15	mr1592	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
vg0715290134	NA	5.28E-12	mr1630	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
vg0715290134	NA	1.81E-06	mr1815	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
vg0715290134	NA	4.77E-24	mr1888	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
vg0715290134	NA	1.56E-08	mr1915	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
vg0715290134	NA	4.43E-08	mr1335_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
vg0715290134	NA	2.55E-07	mr1683_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