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Detailed information for vg0305009028:

Variant ID: vg0305009028 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 5009028
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:

AGAACACGAAGAACAGAGGAAGAACAGGAAGAGAGAGATGGAATTAGAGTTTGAATTGTTGATATTACATTGTTCGATCCAATCTCGGTCTTCCTGTCGG[C/T]
TTTTATAGCAAGACACCATTAAGCCTCTCTCATCTCTCTATTAGTGGCCCAGTCTACAGCTACTGGGTCCACTCACTCACAGGGAAGCGAGAATTCGGCC

Reverse complement sequence

GGCCGAATTCTCGCTTCCCTGTGAGTGAGTGGACCCAGTAGCTGTAGACTGGGCCACTAATAGAGAGATGAGAGAGGCTTAATGGTGTCTTGCTATAAAA[G/A]
CCGACAGGAAGACCGAGATTGGATCGAACAATGTAATATCAACAATTCAAACTCTAATTCCATCTCTCTCTTCCTGTTCTTCCTCTGTTCTTCGTGTTCT

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	74.50%	21.20%	3.75%	0.57%	NA
All Indica	2759	57.40%	35.60%	6.38%	0.54%	NA
All Japonica	1512	99.70%	0.30%	0.00%	0.07%	NA
Aus	269	97.80%	0.00%	0.00%	2.23%	NA
Indica I	595	27.10%	57.00%	15.97%	0.00%	NA
Indica II	465	38.30%	54.60%	7.10%	0.00%	NA
Indica III	913	82.90%	14.70%	0.77%	1.64%	NA
Indica Intermediate	786	62.20%	32.60%	5.22%	0.00%	NA
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.40%	0.00%	0.41%	NA
VI/Aromatic	96	94.80%	1.00%	0.00%	4.17%	NA
Intermediate	90	83.30%	14.40%	1.11%	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
vg0305009028	C -> T	LOC_Os03g09990.1	upstream_gene_variant ; 4062.0bp to feature; MODIFIER	silent_mutation	Average:34.893; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N
vg0305009028	C -> T	LOC_Os03g10000.1	upstream_gene_variant ; 224.0bp to feature; MODIFIER	silent_mutation	Average:34.893; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N
vg0305009028	C -> T	LOC_Os03g10000-LOC_Os03g10010	intergenic_region ; MODIFIER	silent_mutation	Average:34.893; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N
vg0305009028	C -> DEL	N	N	silent_mutation	Average:34.893; 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
vg0305009028	NA	9.15E-12	Heading_date	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
vg0305009028	NA	3.09E-19	Yield	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
vg0305009028	NA	1.53E-08	Yield	Ind_All	YES	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
vg0305009028	NA	1.31E-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
vg0305009028	NA	1.06E-09	mr1352	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
vg0305009028	NA	7.49E-17	mr1583	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
vg0305009028	NA	6.03E-17	mr1870	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
vg0305009028	NA	1.95E-06	mr1870	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
vg0305009028	NA	4.06E-06	mr1881	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
vg0305009028	1.07E-07	NA	mr1103_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
vg0305009028	NA	3.59E-08	mr1212_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
vg0305009028	3.45E-06	2.72E-07	mr1233_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
vg0305009028	1.44E-07	NA	mr1246_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
vg0305009028	1.47E-08	6.39E-08	mr1246_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
vg0305009028	NA	6.00E-06	mr1346_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
vg0305009028	NA	3.10E-06	mr1404_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
vg0305009028	NA	5.81E-06	mr1428_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
vg0305009028	NA	3.03E-06	mr1439_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
vg0305009028	NA	4.27E-06	mr1654_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
vg0305009028	NA	3.02E-13	mr1734_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
vg0305009028	NA	1.03E-13	mr1807_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
vg0305009028	NA	6.14E-08	mr1834_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
vg0305009028	NA	5.02E-20	mr1870_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
vg0305009028	NA	3.52E-07	mr1870_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