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Detailed information for vg0324689010:

Variant ID: vg0324689010 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 24689010
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:

TATATATCTCATTTATACGTGTTTAATTAAGTTGTATCTACGCTTGCCACGTATAAATAAGATCCAGGACAAGCACTTGTGCCAACTTACAGCTTTATAT[C/A]
AATAAAAACAATATGACATAAATTATTTAATTTGATTTGGAGATGGGTATTTCGGACAAAACAAGAATTGCCGAACAATATTTGTTATATATTTGGAGAT

Reverse complement sequence

ATCTCCAAATATATAACAAATATTGTTCGGCAATTCTTGTTTTGTCCGAAATACCCATCTCCAAATCAAATTAAATAATTTATGTCATATTGTTTTTATT[G/T]
ATATAAAGCTGTAAGTTGGCACAAGTGCTTGTCCTGGATCTTATTTATACGTGGCAAGCGTAGATACAACTTAATTAAACACGTATAAATGAGATATATA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	78.80%	21.10%	0.04%	0.00%	NA
All Indica	2759	64.90%	35.00%	0.07%	0.00%	NA
All Japonica	1512	99.60%	0.40%	0.00%	0.00%	NA
Aus	269	98.10%	1.90%	0.00%	0.00%	NA
Indica I	595	85.00%	15.00%	0.00%	0.00%	NA
Indica II	465	19.60%	80.40%	0.00%	0.00%	NA
Indica III	913	75.40%	24.50%	0.11%	0.00%	NA
Indica Intermediate	786	64.40%	35.50%	0.13%	0.00%	NA
Temperate Japonica	767	99.50%	0.50%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	76.70%	23.30%	0.00%	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
vg0324689010	C -> A	LOC_Os03g43960.1	upstream_gene_variant ; 2136.0bp to feature; MODIFIER	silent_mutation	Average:39.414; most accessible tissue: Callus, score: 79.609	N	N	N	N
vg0324689010	C -> A	LOC_Os03g43970.1	downstream_gene_variant ; 4291.0bp to feature; MODIFIER	silent_mutation	Average:39.414; most accessible tissue: Callus, score: 79.609	N	N	N	N
vg0324689010	C -> A	LOC_Os03g43960-LOC_Os03g43970	intergenic_region ; MODIFIER	silent_mutation	Average:39.414; most accessible tissue: Callus, score: 79.609	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0324689010	NA	3.01E-11	Grain_width	Ind_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
vg0324689010	NA	1.91E-07	mr1074	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
vg0324689010	NA	2.42E-07	mr1130	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
vg0324689010	NA	2.94E-12	mr1169	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
vg0324689010	NA	3.99E-09	mr1174	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
vg0324689010	NA	2.96E-10	mr1180	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
vg0324689010	NA	2.28E-13	mr1188	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
vg0324689010	NA	4.28E-09	mr1188	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
vg0324689010	NA	1.69E-06	mr1542	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
vg0324689010	NA	2.47E-09	mr1565	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
vg0324689010	NA	1.52E-06	mr1598	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
vg0324689010	NA	1.77E-06	mr1928	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
vg0324689010	NA	4.63E-06	mr1931	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
vg0324689010	NA	9.77E-06	mr1944	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
vg0324689010	NA	7.61E-13	mr1188_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
vg0324689010	NA	8.34E-08	mr1188_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
vg0324689010	NA	6.62E-08	mr1542_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
vg0324689010	NA	9.41E-06	mr1931_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
vg0324689010	NA	8.06E-07	mr1931_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