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Detailed information for vg0202377139:

Variant ID: vg0202377139 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 2377139
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 124. )

Flanking Sequence (100 bp) in Reference Genome:

CAATTAATAAAAAAAAGAATTTTGGAATTAAAAAATATTATAAGTAGAGTATAGAGTCCATAAAGGAATTTAAAACTAACTAAAATTCGAAATAAACATA[G/A]
TAAAATCAAAAGTAGAGTTTAGAGTCCGTATAAAAATACAATTTACAAACAACTAAAATTCGAAATTAAGAAAAACATGGGAAGAAGAGTTTAAAGTCAA

Reverse complement sequence

TTGACTTTAAACTCTTCTTCCCATGTTTTTCTTAATTTCGAATTTTAGTTGTTTGTAAATTGTATTTTTATACGGACTCTAAACTCTACTTTTGATTTTA[C/T]
TATGTTTATTTCGAATTTTAGTTAGTTTTAAATTCCTTTATGGACTCTATACTCTACTTATAATATTTTTTAATTCCAAAATTCTTTTTTTTATTAATTG

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	69.90%	7.90%	13.92%	8.32%	NA
All Indica	2759	75.20%	0.30%	14.06%	10.40%	NA
All Japonica	1512	63.00%	23.10%	10.19%	3.70%	NA
Aus	269	43.90%	0.00%	39.03%	17.10%	NA
Indica I	595	69.10%	0.00%	17.98%	12.94%	NA
Indica II	465	73.30%	0.60%	14.41%	11.61%	NA
Indica III	913	80.10%	0.10%	11.17%	8.65%	NA
Indica Intermediate	786	75.40%	0.50%	14.25%	9.80%	NA
Temperate Japonica	767	38.10%	39.50%	17.21%	5.22%	NA
Tropical Japonica	504	93.30%	3.20%	2.18%	1.39%	NA
Japonica Intermediate	241	79.30%	12.40%	4.56%	3.73%	NA
VI/Aromatic	96	97.90%	0.00%	2.08%	0.00%	NA
Intermediate	90	68.90%	16.70%	10.00%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0202377139	G -> A	LOC_Os02g05020.1	upstream_gene_variant ; 2759.0bp to feature; MODIFIER	silent_mutation	Average:14.315; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N
vg0202377139	G -> A	LOC_Os02g05000-LOC_Os02g05020	intergenic_region ; MODIFIER	silent_mutation	Average:14.315; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N
vg0202377139	G -> DEL	N	N	silent_mutation	Average:14.315; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0202377139	NA	4.37E-12	Plant_height	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
vg0202377139	NA	1.28E-11	mr1712	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
vg0202377139	NA	5.44E-07	mr1748	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
vg0202377139	NA	1.49E-06	mr1977	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
vg0202377139	NA	2.41E-13	mr1182_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
vg0202377139	NA	5.48E-07	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
vg0202377139	NA	1.07E-07	mr1330_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
vg0202377139	NA	1.18E-07	mr1446_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
vg0202377139	NA	8.76E-09	mr1576_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
vg0202377139	NA	1.20E-06	mr1627_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
vg0202377139	4.63E-06	NA	mr1712_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
vg0202377139	NA	3.77E-09	mr1946_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
vg0202377139	NA	3.77E-09	mr1948_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
vg0202377139	NA	3.26E-08	mr1977_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