Search for Variation information by Variation ID:

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

Detailed information for vg0405835784:

Variant ID: vg0405835784 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 5835784
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.68, G: 0.32, others allele: 0.00, population size: 78. )

Flanking Sequence (100 bp) in Reference Genome:

CAGAAAGAGGAAGGGGGATAGCGGGTCACCTTGCGTCAAACCACGAGTTGGAGCAAATGCAGACAAAAGGGTTCCGTTGAATTTCACTGGGTATCTCACC[A/G]
CGGTTATGCACTCCATAATCCAGCCAACCCACCGATGAGAGAACCCTAGTCTGATCATTGCTTGCTCCAGGTAGTGCCAATCAACCCGATCATACGCCTT

Reverse complement sequence

AAGGCGTATGATCGGGTTGATTGGCACTACCTGGAGCAAGCAATGATCAGACTAGGGTTCTCTCATCGGTGGGTTGGCTGGATTATGGAGTGCATAACCG[T/C]
GGTGAGATACCCAGTGAAATTCAACGGAACCCTTTTGTCTGCATTTGCTCCAACTCGTGGTTTGACGCAAGGTGACCCGCTATCCCCCTTCCTCTTTCTG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	28.60%	2.80%	0.42%	68.26%	NA
All Indica	2759	2.90%	4.60%	0.47%	91.99%	NA
All Japonica	1512	80.20%	0.10%	0.20%	19.58%	NA
Aus	269	7.80%	0.00%	0.00%	92.19%	NA
Indica I	595	3.20%	0.50%	0.17%	96.13%	NA
Indica II	465	3.40%	7.70%	0.65%	88.17%	NA
Indica III	913	1.20%	7.30%	0.66%	90.80%	NA
Indica Intermediate	786	4.50%	2.70%	0.38%	92.49%	NA
Temperate Japonica	767	94.30%	0.00%	0.00%	5.74%	NA
Tropical Japonica	504	56.50%	0.00%	0.40%	43.06%	NA
Japonica Intermediate	241	84.60%	0.40%	0.41%	14.52%	NA
VI/Aromatic	96	7.30%	0.00%	1.04%	91.67%	NA
Intermediate	90	32.20%	2.20%	3.33%	62.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0405835784	A -> DEL	LOC_Os04g10740.1	N	frameshift_variant	Average:15.937; most accessible tissue: Callus, score: 70.492	N	N	N	N
vg0405835784	A -> G	LOC_Os04g10740.1	missense_variant&splice_region_variant ; p.Val712Ala; MODERATE	nonsynonymous_codon ; V712A	Average:15.937; most accessible tissue: Callus, score: 70.492	unknown	unknown	TOLERATED	0.48

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0405835784	NA	3.60E-14	mr1361	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
vg0405835784	1.68E-08	6.28E-10	mr1719	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
vg0405835784	NA	1.12E-07	mr1748_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