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Detailed information for vg0223394543:

Variant ID: vg0223394543 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 23394543
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 336. )

Flanking Sequence (100 bp) in Reference Genome:

CAAACCTTCTTGAACCTGTCATAGGAAAAGCAAATGTGCGAGGTTGACAAGGGCCATTCTCCAAGTATTTCCTTCTCACCCTCTCTCTGAGATTAGGATG[G/A]
TACTCATCAATTTGTTTTCTTAATCCTGGATCATATTTAATCTCATCTTCCCAGTTTATATCATCCAAACATGAATTACATGCATTGTTAGCACTATTCG

Reverse complement sequence

CGAATAGTGCTAACAATGCATGTAATTCATGTTTGGATGATATAAACTGGGAAGATGAGATTAAATATGATCCAGGATTAAGAAAACAAATTGATGAGTA[C/T]
CATCCTAATCTCAGAGAGAGGGTGAGAAGGAAATACTTGGAGAATGGCCCTTGTCAACCTCGCACATTTGCTTTTCCTATGACAGGTTCAAGAAGGTTTG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	92.50%	5.60%	0.19%	1.67%	NA
All Indica	2759	99.70%	0.30%	0.07%	0.00%	NA
All Japonica	1512	80.50%	14.30%	0.40%	4.83%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.40%	0.60%	0.00%	0.00%	NA
Indica III	913	99.80%	0.20%	0.00%	0.00%	NA
Indica Intermediate	786	99.50%	0.30%	0.25%	0.00%	NA
Temperate Japonica	767	98.60%	1.20%	0.00%	0.26%	NA
Tropical Japonica	504	49.60%	36.70%	1.19%	12.50%	NA
Japonica Intermediate	241	87.60%	9.10%	0.00%	3.32%	NA
VI/Aromatic	96	56.20%	36.50%	1.04%	6.25%	NA
Intermediate	90	90.00%	10.00%	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
vg0223394543	G -> A	LOC_Os02g38700.1	synonymous_variant ; p.Tyr226Tyr; LOW	synonymous_codon	Average:41.187; most accessible tissue: Minghui63 panicle, score: 46.754	N	N	N	N
vg0223394543	G -> DEL	LOC_Os02g38700.1	N	frameshift_variant	Average:41.187; most accessible tissue: Minghui63 panicle, score: 46.754	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0223394543	NA	4.04E-06	mr1179	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
vg0223394543	NA	7.07E-08	mr1206	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
vg0223394543	NA	2.99E-07	mr1206	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
vg0223394543	NA	9.20E-06	mr1220	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
vg0223394543	NA	3.51E-06	mr1359	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
vg0223394543	NA	1.10E-06	mr1378	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
vg0223394543	NA	3.59E-07	mr1403	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
vg0223394543	9.56E-06	9.56E-06	mr1663	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
vg0223394543	NA	3.86E-08	mr1668	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
vg0223394543	NA	5.66E-09	mr1671	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
vg0223394543	NA	5.86E-07	mr1798	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
vg0223394543	NA	3.50E-07	mr1951	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
vg0223394543	NA	6.95E-06	mr1668_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
vg0223394543	NA	3.31E-07	mr1671_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