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Detailed information for vg0715259376:

Variant ID: vg0715259376 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 15259376
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.63, A: 0.37, others allele: 0.00, population size: 49. )

Flanking Sequence (100 bp) in Reference Genome:

GGTCACGTTTAGCGGCGACTGATTCGGTGCTAGCCTTCTCCTGTGTCTATGTTCTGGAGCTGTCAGTGTGTGGGTGGTGGTTATTTTCTTCTTTTTCTTG[G/A]
ATACGATCTTCCACGGTTGTAATCTTGTAATTTTTTCCTGCTCTATCAATATGAACTTCGCGCTGTCCGGTGCAAGTTCTTCGGAAAAAAACCTCTAAAG

Reverse complement sequence

CTTTAGAGGTTTTTTTCCGAAGAACTTGCACCGGACAGCGCGAAGTTCATATTGATAGAGCAGGAAAAAATTACAAGATTACAACCGTGGAAGATCGTAT[C/T]
CAAGAAAAAGAAGAAAATAACCACCACCCACACACTGACAGCTCCAGAACATAGACACAGGAGAAGGCTAGCACCGAATCAGTCGCCGCTAAACGTGACC

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	49.30%	46.80%	0.23%	3.66%	NA
All Indica	2759	20.80%	77.20%	0.14%	1.85%	NA
All Japonica	1512	93.60%	0.90%	0.07%	5.49%	NA
Aus	269	87.00%	7.80%	1.12%	4.09%	NA
Indica I	595	11.10%	88.60%	0.17%	0.17%	NA
Indica II	465	13.50%	85.80%	0.00%	0.65%	NA
Indica III	913	18.20%	81.40%	0.22%	0.22%	NA
Indica Intermediate	786	35.40%	58.80%	0.13%	5.73%	NA
Temperate Japonica	767	88.30%	1.20%	0.13%	10.43%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	97.90%	0.80%	0.00%	1.24%	NA
VI/Aromatic	96	54.20%	14.60%	3.12%	28.12%	NA
Intermediate	90	64.40%	34.40%	0.00%	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
vg0715259376	G -> DEL	N	N	silent_mutation	Average:43.793; most accessible tissue: Zhenshan97 young leaf, score: 72.34	N	N	N	N
vg0715259376	G -> A	LOC_Os07g26500-LOC_Os07g26510	intergenic_region ; MODIFIER	silent_mutation	Average:43.793; most accessible tissue: Zhenshan97 young leaf, score: 72.34	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0715259376	NA	3.98E-22	mr1131	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
vg0715259376	NA	5.17E-19	mr1199	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
vg0715259376	NA	2.30E-11	mr1233	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
vg0715259376	NA	2.08E-24	mr1264	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
vg0715259376	NA	1.18E-09	mr1379	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
vg0715259376	NA	1.54E-08	mr1457	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
vg0715259376	NA	3.29E-08	mr1559	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
vg0715259376	NA	1.17E-13	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
vg0715259376	NA	2.23E-11	mr1657	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
vg0715259376	NA	4.14E-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
vg0715259376	NA	1.09E-18	mr1131_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
vg0715259376	NA	2.72E-17	mr1199_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
vg0715259376	NA	1.04E-07	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