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Detailed information for vg0706102792:

Variant ID: vg0706102792 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 6102792
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACTTTGACTTCTTAATTCTATAAAAATATTTATTAAAAAGTGATATATGTATACTTGTATGAAAGTATTTTTCAAGACCAATCTATTCATATAATTTTTA[T/C]
ATTTTCAAACTCAATAACTTAAGAGTTATTCATGATTTATATTCCCAAGGTTTGACTTAAACATTGTCCTAAACGACTTCCTTTACGAGTACGGAGGAGT

Reverse complement sequence

ACTCCTCCGTACTCGTAAAGGAAGTCGTTTAGGACAATGTTTAAGTCAAACCTTGGGAATATAAATCATGAATAACTCTTAAGTTATTGAGTTTGAAAAT[A/G]
TAAAAATTATATGAATAGATTGGTCTTGAAAAATACTTTCATACAAGTATACATATATCACTTTTTAATAAATATTTTTATAGAATTAAGAAGTCAAAGT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	83.10%	13.40%	3.49%	0.00%	NA
All Indica	2759	97.60%	1.30%	1.05%	0.00%	NA
All Japonica	1512	52.70%	38.60%	8.73%	0.00%	NA
Aus	269	99.60%	0.00%	0.37%	0.00%	NA
Indica I	595	96.80%	2.00%	1.18%	0.00%	NA
Indica II	465	95.10%	3.20%	1.72%	0.00%	NA
Indica III	913	99.80%	0.10%	0.11%	0.00%	NA
Indica Intermediate	786	97.20%	1.10%	1.65%	0.00%	NA
Temperate Japonica	767	29.70%	57.90%	12.39%	0.00%	NA
Tropical Japonica	504	87.10%	8.90%	3.97%	0.00%	NA
Japonica Intermediate	241	53.90%	39.00%	7.05%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	84.40%	12.20%	3.33%	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
vg0706102792	T -> C	LOC_Os07g11050-LOC_Os07g11060	intergenic_region ; MODIFIER	silent_mutation	Average:36.574; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0706102792	9.15E-06	NA	mr1115	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
vg0706102792	NA	1.49E-08	mr1252	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
vg0706102792	8.54E-06	2.20E-06	mr1387	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
vg0706102792	7.75E-06	7.73E-06	mr1494	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
vg0706102792	NA	6.68E-06	mr1503	Jap_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
vg0706102792	NA	2.06E-11	mr1626	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
vg0706102792	NA	2.88E-07	mr1654	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
vg0706102792	2.12E-08	NA	mr1773	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
vg0706102792	6.68E-06	6.67E-06	mr1773	Jap_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
vg0706102792	6.86E-06	NA	mr1811	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
vg0706102792	7.47E-08	6.42E-06	mr1816	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
vg0706102792	NA	1.46E-06	mr1880	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
vg0706102792	NA	7.67E-08	mr1182_2	Jap_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
vg0706102792	NA	1.18E-06	mr1282_2	Jap_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