Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0224380737:

Variant ID: vg0224380737 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 24380737
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCCAGTCAGGCCGAGAGCCGATAGGTCGCGTAGAACCATCCCGAATGAATTGAAAAGAAAAGAAAAGAAAAAAAAATCTAACTGTGACATCAAATACAGA[G/A]
TACAAAGATATACAGCTGGTACTCGTATCAATTATTTATATATTAAATCTAAAAACTGTGTATACAATACAGAATTATATACGAGAGCATATATAAGAGA

Reverse complement sequence

TCTCTTATATATGCTCTCGTATATAATTCTGTATTGTATACACAGTTTTTAGATTTAATATATAAATAATTGATACGAGTACCAGCTGTATATCTTTGTA[C/T]
TCTGTATTTGATGTCACAGTTAGATTTTTTTTTCTTTTCTTTTCTTTTCAATTCATTCGGGATGGTTCTACGCGACCTATCGGCTCTCGGCCTGACTGGC

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	95.20%	1.10%	2.50%	1.12%	NA
All Indica	2759	94.30%	1.60%	2.86%	1.23%	NA
All Japonica	1512	97.40%	0.60%	1.46%	0.53%	NA
Aus	269	98.50%	0.00%	0.74%	0.74%	NA
Indica I	595	90.90%	5.40%	2.69%	1.01%	NA
Indica II	465	95.90%	0.40%	2.80%	0.86%	NA
Indica III	913	95.20%	0.30%	3.40%	1.10%	NA
Indica Intermediate	786	94.80%	1.00%	2.42%	1.78%	NA
Temperate Japonica	767	99.30%	0.40%	0.13%	0.13%	NA
Tropical Japonica	504	96.20%	0.20%	2.38%	1.19%	NA
Japonica Intermediate	241	93.80%	2.10%	3.73%	0.41%	NA
VI/Aromatic	96	75.00%	0.00%	15.62%	9.38%	NA
Intermediate	90	100.00%	0.00%	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
vg0224380737	G -> A	LOC_Os02g40270.1	downstream_gene_variant ; 154.0bp to feature; MODIFIER	silent_mutation	Average:77.776; most accessible tissue: Callus, score: 93.333	N	N	N	N
vg0224380737	G -> A	LOC_Os02g40260-LOC_Os02g40270	intergenic_region ; MODIFIER	silent_mutation	Average:77.776; most accessible tissue: Callus, score: 93.333	N	N	N	N
vg0224380737	G -> DEL	N	N	silent_mutation	Average:77.776; most accessible tissue: Callus, score: 93.333	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0224380737	NA	9.51E-06	mr1629_2	Ind_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
vg0224380737	NA	9.95E-06	mr1734_2	Ind_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