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Detailed information for vg0224723022:

Variant ID: vg0224723022 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 24723022
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CATGTAAAACAAAGCCACTTATTAGCAAATGATAAATTAGGGCTAATTATTTTTTTAAAAAAACAGATTAATGTGATTTTTTAAAAAAAGCTTTTCTATA[G/T]
AAAACTTTTTATAAAAAAGCATTGTTTAATAGATTGAGAAGCGTGCGCGTGGAAAAACAAGTAGGATGGAGTTGAGAATATTGAGTAAAGAAACACAGCC

Reverse complement sequence

GGCTGTGTTTCTTTACTCAATATTCTCAACTCCATCCTACTTGTTTTTCCACGCGCACGCTTCTCAATCTATTAAACAATGCTTTTTTATAAAAAGTTTT[C/A]
TATAGAAAAGCTTTTTTTAAAAAATCACATTAATCTGTTTTTTTAAAAAAATAATTAGCCCTAATTTATCATTTGCTAATAAGTGGCTTTGTTTTACATG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	95.60%	4.20%	0.23%	0.00%	NA
All Indica	2759	96.10%	3.70%	0.18%	0.00%	NA
All Japonica	1512	95.80%	3.90%	0.33%	0.00%	NA
Aus	269	87.40%	12.30%	0.37%	0.00%	NA
Indica I	595	94.30%	5.40%	0.34%	0.00%	NA
Indica II	465	99.60%	0.40%	0.00%	0.00%	NA
Indica III	913	96.10%	3.90%	0.00%	0.00%	NA
Indica Intermediate	786	95.40%	4.20%	0.38%	0.00%	NA
Temperate Japonica	767	94.70%	5.20%	0.13%	0.00%	NA
Tropical Japonica	504	98.20%	1.80%	0.00%	0.00%	NA
Japonica Intermediate	241	94.20%	4.10%	1.66%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	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
vg0224723022	G -> T	LOC_Os02g40800.1	upstream_gene_variant ; 1812.0bp to feature; MODIFIER	silent_mutation	Average:67.966; most accessible tissue: Minghui63 panicle, score: 86.442	N	N	N	N
vg0224723022	G -> T	LOC_Os02g40784.1	intron_variant ; MODIFIER	silent_mutation	Average:67.966; most accessible tissue: Minghui63 panicle, score: 86.442	N	N	N	N
vg0224723022	G -> T	LOC_Os02g40784.3	intron_variant ; MODIFIER	silent_mutation	Average:67.966; most accessible tissue: Minghui63 panicle, score: 86.442	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0224723022	2.49E-06	2.49E-06	mr1172_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