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Detailed information for vg0328780990:

Variant ID: vg0328780990 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 28780990
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:

TAAGTTATATGTCACATACCAAAATATGCAATTTTGTACAACTTGGATCATAATAATATGGGGTTTTACGAAATGTACTCTTAAATTTACGCTGTGGCTG[A/G]
TACTCCCTCTGTCCCGAAATATAAGGGATTTTGGTTGGATGTGACACATTCTAGTACTATGAATTTGGACAAAGAGTATGTCCAAATTCACAGTCGCAGG

Reverse complement sequence

CCTGCGACTGTGAATTTGGACATACTCTTTGTCCAAATTCATAGTACTAGAATGTGTCACATCCAACCAAAATCCCTTATATTTCGGGACAGAGGGAGTA[T/C]
CAGCCACAGCGTAAATTTAAGAGTACATTTCGTAAAACCCCATATTATTATGATCCAAGTTGTACAAAATTGCATATTTTGGTATGTGACATATAACTTA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	94.00%	4.30%	1.65%	0.00%	NA
All Indica	2759	98.30%	0.20%	1.49%	0.00%	NA
All Japonica	1512	84.50%	13.20%	2.38%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	95.10%	0.30%	4.54%	0.00%	NA
Indica II	465	99.80%	0.00%	0.22%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	98.00%	0.40%	1.65%	0.00%	NA
Temperate Japonica	767	74.70%	21.10%	4.17%	0.00%	NA
Tropical Japonica	504	98.60%	1.40%	0.00%	0.00%	NA
Japonica Intermediate	241	85.90%	12.40%	1.66%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	1.10%	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
vg0328780990	A -> G	LOC_Os03g50440.1	upstream_gene_variant ; 470.0bp to feature; MODIFIER	silent_mutation	Average:60.911; most accessible tissue: Minghui63 panicle, score: 82.797	N	N	N	N
vg0328780990	A -> G	LOC_Os03g50430.1	downstream_gene_variant ; 3742.0bp to feature; MODIFIER	silent_mutation	Average:60.911; most accessible tissue: Minghui63 panicle, score: 82.797	N	N	N	N
vg0328780990	A -> G	LOC_Os03g50430-LOC_Os03g50440	intergenic_region ; MODIFIER	silent_mutation	Average:60.911; most accessible tissue: Minghui63 panicle, score: 82.797	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0328780990	NA	1.67E-11	Heading_date	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
vg0328780990	1.70E-06	NA	mr1586	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
vg0328780990	3.39E-06	4.30E-07	mr1060_2	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
vg0328780990	2.03E-06	3.67E-08	mr1060_2	Jap_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
vg0328780990	NA	6.96E-06	mr1296_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
vg0328780990	8.83E-06	NA	mr1310_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
vg0328780990	NA	1.07E-06	mr1321_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
vg0328780990	NA	1.21E-06	mr1355_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
vg0328780990	NA	5.89E-07	mr1358_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
vg0328780990	NA	1.23E-06	mr1358_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
vg0328780990	NA	9.98E-06	mr1452_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
vg0328780990	NA	8.00E-08	mr1568_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
vg0328780990	5.50E-06	5.50E-06	mr1568_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
vg0328780990	NA	6.37E-06	mr1686_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
vg0328780990	NA	5.29E-08	mr1749_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
vg0328780990	8.51E-07	3.41E-10	mr1821_2	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
vg0328780990	9.04E-06	NA	mr1959_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