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Detailed information for vg0224209424:

Variant ID: vg0224209424 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 24209424
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGGAGCTAGGTGAATAGATCCATGCAATAGCAGTAAAGTTTTTTTTTTCTAACGTCAGGCTACTGCCAACGTTTTATATAAAGAAGGTGTCTCATTTTAA[G/A]
AAGTAAACATAATTAAATTTTACAGTGCCTAATTAATTAGGAAAAACTGAGCGAAAACTATAACTACAATAACACACCAACAGCTAACCTAACCTAAGCT

Reverse complement sequence

AGCTTAGGTTAGGTTAGCTGTTGGTGTGTTATTGTAGTTATAGTTTTCGCTCAGTTTTTCCTAATTAATTAGGCACTGTAAAATTTAATTATGTTTACTT[C/T]
TTAAAATGAGACACCTTCTTTATATAAAACGTTGGCAGTAGCCTGACGTTAGAAAAAAAAAACTTTACTGCTATTGCATGGATCTATTCACCTAGCTCCC

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	97.70%	1.90%	0.38%	0.00%	NA
All Indica	2759	99.30%	0.40%	0.22%	0.00%	NA
All Japonica	1512	94.50%	4.70%	0.79%	0.00%	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	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	98.90%	1.00%	0.11%	0.00%	NA
Indica Intermediate	786	99.00%	0.40%	0.64%	0.00%	NA
Temperate Japonica	767	95.20%	3.80%	1.04%	0.00%	NA
Tropical Japonica	504	98.20%	1.40%	0.40%	0.00%	NA
Japonica Intermediate	241	84.60%	14.50%	0.83%	0.00%	NA
VI/Aromatic	96	92.70%	7.30%	0.00%	0.00%	NA
Intermediate	90	97.80%	2.20%	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
vg0224209424	G -> A	LOC_Os02g40000-LOC_Os02g40010	intergenic_region ; MODIFIER	silent_mutation	Average:50.911; most accessible tissue: Zhenshan97 panicle, score: 71.253	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0224209424	7.35E-07	3.42E-06	mr1101	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
vg0224209424	9.60E-06	6.34E-06	mr1113	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
vg0224209424	NA	5.89E-06	mr1117	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
vg0224209424	3.07E-07	4.10E-08	mr1123	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
vg0224209424	4.95E-06	NA	mr1150	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
vg0224209424	1.41E-06	4.68E-07	mr1247	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
vg0224209424	NA	5.78E-06	mr1495	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
vg0224209424	1.13E-06	3.75E-07	mr1496	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
vg0224209424	4.13E-06	7.24E-06	mr1858	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
vg0224209424	4.13E-06	7.24E-06	mr1859	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
vg0224209424	3.79E-07	1.84E-07	mr1917	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
vg0224209424	1.35E-08	1.54E-08	mr1936	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
vg0224209424	NA	6.85E-06	mr1247_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