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Detailed information for vg0221768176:

Variant ID: vg0221768176 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 21768176
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGTGATGAACGCTGCAGCACAGGAAAGAACTCGAGGCAAGTATAAGGAAGCAGCTCCAAGGAGTGGAATTATCACCATCCCCATATGACACTGCATGGGT[A/G]
GCTATGGTGCCACTCCGGGGTTCGTCTCACAATCCAAGCTTCCCTCAATGCGTCGACTGGATACTAGAGAATCAATGGGACGATGGATCATGGAGTATTG

Reverse complement sequence

CAATACTCCATGATCCATCGTCCCATTGATTCTCTAGTATCCAGTCGACGCATTGAGGGAAGCTTGGATTGTGAGACGAACCCCGGAGTGGCACCATAGC[T/C]
ACCCATGCAGTGTCATATGGGGATGGTGATAATTCCACTCCTTGGAGCTGCTTCCTTATACTTGCCTCGAGTTCTTTCCTGTGCTGCAGCGTTCATCACA

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	66.50%	33.20%	0.30%	0.00%	NA
All Indica	2759	97.50%	2.20%	0.25%	0.00%	NA
All Japonica	1512	8.50%	91.20%	0.33%	0.00%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	98.30%	1.30%	0.34%	0.00%	NA
Indica II	465	98.90%	0.90%	0.22%	0.00%	NA
Indica III	913	98.20%	1.80%	0.00%	0.00%	NA
Indica Intermediate	786	95.30%	4.20%	0.51%	0.00%	NA
Temperate Japonica	767	2.20%	97.30%	0.52%	0.00%	NA
Tropical Japonica	504	19.40%	80.60%	0.00%	0.00%	NA
Japonica Intermediate	241	5.40%	94.20%	0.41%	0.00%	NA
VI/Aromatic	96	11.50%	87.50%	1.04%	0.00%	NA
Intermediate	90	51.10%	47.80%	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
vg0221768176	A -> G	LOC_Os02g36140.2	synonymous_variant ; p.Val111Val; LOW	synonymous_codon	Average:69.017; most accessible tissue: Callus, score: 83.865	N	N	N	N
vg0221768176	A -> G	LOC_Os02g36140.5	synonymous_variant ; p.Val111Val; LOW	synonymous_codon	Average:69.017; most accessible tissue: Callus, score: 83.865	N	N	N	N
vg0221768176	A -> G	LOC_Os02g36140.4	synonymous_variant ; p.Val111Val; LOW	synonymous_codon	Average:69.017; most accessible tissue: Callus, score: 83.865	N	N	N	N
vg0221768176	A -> G	LOC_Os02g36140.3	synonymous_variant ; p.Val111Val; LOW	synonymous_codon	Average:69.017; most accessible tissue: Callus, score: 83.865	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0221768176	NA	1.32E-40	mr1124	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
vg0221768176	NA	9.79E-29	mr1202	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
vg0221768176	NA	1.17E-08	mr1302	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
vg0221768176	NA	4.72E-12	mr1386	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
vg0221768176	NA	1.50E-06	mr1392	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
vg0221768176	NA	4.90E-14	mr1592	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
vg0221768176	NA	2.28E-06	mr1646	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
vg0221768176	NA	9.18E-14	mr1653	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
vg0221768176	NA	5.02E-11	mr1714	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
vg0221768176	7.70E-06	2.12E-07	mr1961	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
vg0221768176	NA	3.49E-38	mr1072_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
vg0221768176	NA	5.73E-38	mr1075_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
vg0221768176	NA	5.17E-10	mr1595_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
vg0221768176	NA	2.41E-08	mr1600_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
vg0221768176	NA	1.74E-06	mr1691_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