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Detailed information for vg0715846947:

Variant ID: vg0715846947 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 15846947
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTAGCAGCGAGGTATTCGTGATGACTTCATTAAATCTAAAGATATATCCATCTAGTTTTTCAGAGATACTCATAGGGGTAGGTGTGCGCGTGTGTTCATA[G/A]
GGTGTTGTAAGCTTCTTTATTTGTACTGTGTTTCTTAAGAACAAAAATAAGGACGAAAAGTTTTATTTCCATATGATTACTGAGATATCGTTGGGTGAGG

Reverse complement sequence

CCTCACCCAACGATATCTCAGTAATCATATGGAAATAAAACTTTTCGTCCTTATTTTTGTTCTTAAGAAACACAGTACAAATAAAGAAGCTTACAACACC[C/T]
TATGAACACACGCGCACACCTACCCCTATGAGTATCTCTGAAAAACTAGATGGATATATCTTTAGATTTAATGAAGTCATCACGAATACCTCGCTGCTAA

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	64.60%	34.80%	0.00%	0.59%	NA
All Indica	2759	96.30%	3.20%	0.00%	0.51%	NA
All Japonica	1512	6.70%	93.10%	0.00%	0.20%	NA
Aus	269	88.50%	8.90%	0.00%	2.60%	NA
Indica I	595	98.80%	0.80%	0.00%	0.34%	NA
Indica II	465	95.50%	3.90%	0.00%	0.65%	NA
Indica III	913	99.00%	0.80%	0.00%	0.22%	NA
Indica Intermediate	786	91.70%	7.40%	0.00%	0.89%	NA
Temperate Japonica	767	11.50%	88.50%	0.00%	0.00%	NA
Tropical Japonica	504	2.00%	98.00%	0.00%	0.00%	NA
Japonica Intermediate	241	1.70%	97.10%	0.00%	1.24%	NA
VI/Aromatic	96	8.30%	90.60%	0.00%	1.04%	NA
Intermediate	90	52.20%	44.40%	0.00%	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
vg0715846947	G -> DEL	N	N	silent_mutation	Average:50.401; most accessible tissue: Callus, score: 74.318	N	N	N	N
vg0715846947	G -> A	LOC_Os07g27250.1	upstream_gene_variant ; 4979.0bp to feature; MODIFIER	silent_mutation	Average:50.401; most accessible tissue: Callus, score: 74.318	N	N	N	N
vg0715846947	G -> A	LOC_Os07g27260.1	upstream_gene_variant ; 453.0bp to feature; MODIFIER	silent_mutation	Average:50.401; most accessible tissue: Callus, score: 74.318	N	N	N	N
vg0715846947	G -> A	LOC_Os07g27250-LOC_Os07g27260	intergenic_region ; MODIFIER	silent_mutation	Average:50.401; most accessible tissue: Callus, score: 74.318	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0715846947	NA	1.77E-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
vg0715846947	NA	7.66E-16	mr1484	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
vg0715846947	NA	1.46E-17	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
vg0715846947	4.77E-06	NA	mr1719	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
vg0715846947	NA	2.62E-07	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
vg0715846947	NA	6.65E-10	mr1945	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
vg0715846947	NA	4.47E-18	mr1281_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
vg0715846947	NA	1.87E-33	mr1841_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
vg0715846947	NA	1.27E-18	mr1945_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