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Detailed information for vg0222830353:

Variant ID: vg0222830353 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 22830353
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTACGGATAAAAAGTGAAAGATAGGAGACAAAAGTATATCACAAGTGAAATAGCAAAAACCATTAATTTAATCTTACATATAGGTACTCCCTCCGTCCCA[C/T]
AATATAAGGGATTTTGAGTTTTTTGTTTGTAACGTTTTACCACTCATTTTATTCAAATTTTTTTTTGCAAATATAAAAAAATAAAAAATTGTACTTAAAG

Reverse complement sequence

CTTTAAGTACAATTTTTTATTTTTTTATATTTGCAAAAAAAAATTTGAATAAAATGAGTGGTAAAACGTTACAAACAAAAAACTCAAAATCCCTTATATT[G/A]
TGGGACGGAGGGAGTACCTATATGTAAGATTAAATTAATGGTTTTTGCTATTTCACTTGTGATATACTTTTGTCTCCTATCTTTCACTTTTTATCCGTAG

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	92.80%	4.10%	3.11%	0.00%	NA
All Indica	2759	99.10%	0.20%	0.76%	0.00%	NA
All Japonica	1512	79.60%	12.20%	8.20%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	97.80%	0.20%	2.02%	0.00%	NA
Indica II	465	99.60%	0.00%	0.43%	0.00%	NA
Indica III	913	99.60%	0.30%	0.11%	0.00%	NA
Indica Intermediate	786	99.10%	0.10%	0.76%	0.00%	NA
Temperate Japonica	767	66.90%	19.70%	13.43%	0.00%	NA
Tropical Japonica	504	98.40%	0.00%	1.59%	0.00%	NA
Japonica Intermediate	241	80.90%	13.70%	5.39%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	93.30%	4.40%	2.22%	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
vg0222830353	C -> T	LOC_Os02g37830.1	upstream_gene_variant ; 4133.0bp to feature; MODIFIER	silent_mutation	Average:51.639; most accessible tissue: Minghui63 panicle, score: 70.194	N	N	N	N
vg0222830353	C -> T	LOC_Os02g37830.2	upstream_gene_variant ; 4133.0bp to feature; MODIFIER	silent_mutation	Average:51.639; most accessible tissue: Minghui63 panicle, score: 70.194	N	N	N	N
vg0222830353	C -> T	LOC_Os02g37830-LOC_Os02g37834	intergenic_region ; MODIFIER	silent_mutation	Average:51.639; most accessible tissue: Minghui63 panicle, score: 70.194	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0222830353	8.19E-10	NA	mr1210	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
vg0222830353	3.96E-06	1.02E-09	mr1210	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
vg0222830353	3.90E-10	NA	mr1305	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
vg0222830353	9.38E-07	1.05E-09	mr1305	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
vg0222830353	3.54E-06	3.54E-06	mr1409	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
vg0222830353	8.26E-10	9.52E-09	mr1585	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
vg0222830353	3.52E-07	2.08E-12	mr1585	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
vg0222830353	8.22E-13	NA	mr1586	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
vg0222830353	1.42E-07	8.82E-11	mr1586	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
vg0222830353	1.26E-06	NA	mr1765	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
vg0222830353	NA	1.36E-07	mr1765	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
vg0222830353	1.77E-06	NA	mr1305_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
vg0222830353	NA	5.09E-07	mr1305_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
vg0222830353	6.02E-07	1.34E-07	mr1585_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
vg0222830353	NA	2.47E-08	mr1585_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