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Detailed information for vg0106679567:

Variant ID: vg0106679567 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 6679567
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, C: 0.01, others allele: 0.00, population size: 126. )

Flanking Sequence (100 bp) in Reference Genome:

ATCTAGACTGTTTGAAGAGCTTTTATTTCTGGAAGAAGTTACAACTGCCAGAAGCTCCTAAACAAGCCCCTAGACTAGAACTAAAGATTTTGGAAGAAAC[T/C]
ATATTTGCTAGAAGCTCTCCAAACATGATCTTAATACAAAACAAATCATAGAACATGCATAGAGATATTCTAAGTACCTATTTATAACATTGGGAAAAAC

Reverse complement sequence

GTTTTTCCCAATGTTATAAATAGGTACTTAGAATATCTCTATGCATGTTCTATGATTTGTTTTGTATTAAGATCATGTTTGGAGAGCTTCTAGCAAATAT[A/G]
GTTTCTTCCAAAATCTTTAGTTCTAGTCTAGGGGCTTGTTTAGGAGCTTCTGGCAGTTGTAACTTCTTCCAGAAATAAAAGCTCTTCAAACAGTCTAGAT

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	78.20%	21.40%	0.36%	0.00%	NA
All Indica	2759	74.30%	25.60%	0.18%	0.00%	NA
All Japonica	1512	82.10%	17.30%	0.66%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	97.80%	2.20%	0.00%	0.00%	NA
Indica II	465	53.10%	46.70%	0.22%	0.00%	NA
Indica III	913	71.30%	28.60%	0.11%	0.00%	NA
Indica Intermediate	786	72.40%	27.20%	0.38%	0.00%	NA
Temperate Japonica	767	92.30%	6.60%	1.04%	0.00%	NA
Tropical Japonica	504	67.10%	32.90%	0.00%	0.00%	NA
Japonica Intermediate	241	80.90%	18.30%	0.83%	0.00%	NA
VI/Aromatic	96	80.20%	19.80%	0.00%	0.00%	NA
Intermediate	90	67.80%	30.00%	2.22%	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
vg0106679567	T -> C	LOC_Os01g12230-LOC_Os01g12240	intergenic_region ; MODIFIER	silent_mutation	Average:30.222; most accessible tissue: Callus, score: 67.56	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0106679567	NA	9.04E-06	Grain_weight	Jap_All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0106679567	NA	2.74E-06	mr1236	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
vg0106679567	5.48E-07	NA	mr1498	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
vg0106679567	1.39E-08	NA	mr1769	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
vg0106679567	7.32E-06	NA	mr1769	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
vg0106679567	1.92E-06	NA	mr1951	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
vg0106679567	NA	6.60E-06	mr1219_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
vg0106679567	NA	3.70E-07	mr1236_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
vg0106679567	NA	5.66E-07	mr1236_2	Ind_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
vg0106679567	5.58E-07	NA	mr1498_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
vg0106679567	NA	2.95E-07	mr1498_2	Ind_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
vg0106679567	3.20E-07	NA	mr1769_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
vg0106679567	9.26E-06	NA	mr1925_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
vg0106679567	NA	1.22E-06	mr1925_2	Ind_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