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Detailed information for vg0224555817:

Variant ID: vg0224555817 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 24555817
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TATATATATATATATATATATTTGTGTGAAAAAATTGAATAAGACAAATGGTACAATATTTGATAAAAAACTAATAGTGTCATATATTAAAGAAACGGAT[G/A]
TAGTATCATAGTGCTACCAGAGTACAAATTTGCAACGTATGTCTAGAAAAAGTGTCCTAATGCATCAATATTCAGCCCAAAAAGGGCTTATGATGTTAGG

Reverse complement sequence

CCTAACATCATAAGCCCTTTTTGGGCTGAATATTGATGCATTAGGACACTTTTTCTAGACATACGTTGCAAATTTGTACTCTGGTAGCACTATGATACTA[C/T]
ATCCGTTTCTTTAATATATGACACTATTAGTTTTTTATCAAATATTGTACCATTTGTCTTATTCAATTTTTTCACACAAATATATATATATATATATATA

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	93.70%	0.10%	0.53%	5.67%	NA
All Indica	2759	97.40%	0.00%	0.62%	2.03%	NA
All Japonica	1512	86.70%	0.30%	0.53%	12.50%	NA
Aus	269	98.10%	0.00%	0.00%	1.86%	NA
Indica I	595	99.20%	0.00%	0.67%	0.17%	NA
Indica II	465	98.50%	0.00%	0.00%	1.51%	NA
Indica III	913	96.50%	0.00%	0.66%	2.85%	NA
Indica Intermediate	786	96.30%	0.00%	0.89%	2.80%	NA
Temperate Japonica	767	81.10%	0.10%	0.78%	17.99%	NA
Tropical Japonica	504	94.60%	0.40%	0.20%	4.76%	NA
Japonica Intermediate	241	88.00%	0.40%	0.41%	11.20%	NA
VI/Aromatic	96	90.60%	0.00%	0.00%	9.38%	NA
Intermediate	90	88.90%	1.10%	0.00%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0224555817	G -> A	LOC_Os02g40490.1	upstream_gene_variant ; 4359.0bp to feature; MODIFIER	silent_mutation	Average:56.809; most accessible tissue: Minghui63 root, score: 74.1	N	N	N	N
vg0224555817	G -> A	LOC_Os02g40480-LOC_Os02g40490	intergenic_region ; MODIFIER	silent_mutation	Average:56.809; most accessible tissue: Minghui63 root, score: 74.1	N	N	N	N
vg0224555817	G -> DEL	N	N	silent_mutation	Average:56.809; most accessible tissue: Minghui63 root, score: 74.1	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0224555817	NA	1.27E-06	mr1031	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
vg0224555817	NA	2.15E-08	mr1723	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
vg0224555817	NA	3.71E-06	mr1788	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
vg0224555817	1.26E-06	NA	mr1238_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
vg0224555817	1.51E-06	NA	mr1484_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
vg0224555817	NA	2.89E-06	mr1723_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
vg0224555817	1.97E-06	NA	mr1945_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
vg0224555817	5.42E-07	9.97E-07	mr1986_2	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