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Detailed information for vg0607507935:

Variant ID: vg0607507935 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 7507935
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:

GCAAACAGCTACACGTTCGTACCATTTTGACGTGATGATATATGCAGATGAAAAACCGATGGACAATCGAGTTGGATATAGAGATAAATTGAATATGTAC[C/T]
GTTTTCTCTGATCATCATTGTCTATAAAAATTTTCTTCAGTAACAGATACTTGATGTGGTGGGTTTTGACTATCGGAGTATTCATCTTATTTAAAAATTT

Reverse complement sequence

AAATTTTTAAATAAGATGAATACTCCGATAGTCAAAACCCACCACATCAAGTATCTGTTACTGAAGAAAATTTTTATAGACAATGATGATCAGAGAAAAC[G/A]
GTACATATTCAATTTATCTCTATATCCAACTCGATTGTCCATCGGTTTTTCATCTGCATATATCATCACGTCAAAATGGTACGAACGTGTAGCTGTTTGC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	62.30%	37.30%	0.40%	0.00%	NA
All Indica	2759	97.20%	2.30%	0.43%	0.00%	NA
All Japonica	1512	3.50%	96.10%	0.40%	0.00%	NA
Aus	269	30.50%	69.50%	0.00%	0.00%	NA
Indica I	595	98.30%	0.70%	1.01%	0.00%	NA
Indica II	465	97.20%	2.60%	0.22%	0.00%	NA
Indica III	913	98.70%	1.10%	0.22%	0.00%	NA
Indica Intermediate	786	94.80%	4.80%	0.38%	0.00%	NA
Temperate Japonica	767	4.00%	95.20%	0.78%	0.00%	NA
Tropical Japonica	504	1.40%	98.60%	0.00%	0.00%	NA
Japonica Intermediate	241	6.20%	93.80%	0.00%	0.00%	NA
VI/Aromatic	96	85.40%	14.60%	0.00%	0.00%	NA
Intermediate	90	48.90%	50.00%	1.11%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0607507935	C -> T	LOC_Os06g13580-LOC_Os06g13590	intergenic_region ; MODIFIER	silent_mutation	Average:64.274; most accessible tissue: Callus, score: 92.531	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0607507935	NA	1.29E-17	mr1253	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
vg0607507935	NA	1.14E-12	mr1449	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
vg0607507935	NA	3.99E-07	mr1527	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
vg0607507935	NA	1.16E-10	mr1228_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
vg0607507935	NA	2.86E-12	mr1325_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
vg0607507935	NA	2.07E-11	mr1338_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
vg0607507935	NA	1.63E-06	mr1405_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
vg0607507935	NA	2.30E-09	mr1506_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
vg0607507935	NA	3.87E-09	mr1527_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
vg0607507935	4.96E-06	NA	mr1577_2	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
vg0607507935	NA	6.74E-15	mr1686_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
vg0607507935	NA	4.12E-17	mr1744_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
vg0607507935	NA	8.08E-06	mr1786_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