Search for Variation information by Variation ID:

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

Detailed information for vg0142041116:

Variant ID: vg0142041116 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 42041116
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:

ACTAGGTGATACACTAATATTTGGTGGGAGATCTAAAGTTAGAAATTTCTATGTTCTTACCCAAGAAAATCATTCCAATGTTAGCTTTTACCAAACACCT[G/A]
CAACCAGTGATGGACAAGTTGCAATCAAGGTTAGCGGGATGGAAAGGGAAGTTAATCCAGCAATCAGGGCGGAAGACGCTAGTCACGTATGTTCTCAGCT

Reverse complement sequence

AGCTGAGAACATACGTGACTAGCGTCTTCCGCCCTGATTGCTGGATTAACTTCCCTTTCCATCCCGCTAACCTTGATTGCAACTTGTCCATCACTGGTTG[C/T]
AGGTGTTTGGTAAAAGCTAACATTGGAATGATTTTCTTGGGTAAGAACATAGAAATTTCTAACTTTAGATCTCCCACCAAATATTAGTGTATCACCTAGT

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	95.90%	4.00%	0.06%	0.00%	NA
All Indica	2759	93.30%	6.60%	0.07%	0.00%	NA
All Japonica	1512	99.70%	0.30%	0.00%	0.00%	NA
Aus	269	98.90%	1.10%	0.00%	0.00%	NA
Indica I	595	85.20%	14.60%	0.17%	0.00%	NA
Indica II	465	98.90%	1.10%	0.00%	0.00%	NA
Indica III	913	94.70%	5.30%	0.00%	0.00%	NA
Indica Intermediate	786	94.50%	5.30%	0.13%	0.00%	NA
Temperate Japonica	767	99.60%	0.40%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	96.70%	2.20%	1.11%	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
vg0142041116	G -> A	LOC_Os01g72490.1	upstream_gene_variant ; 1494.0bp to feature; MODIFIER	silent_mutation	Average:51.596; most accessible tissue: Zhenshan97 panicle, score: 68.538	N	N	N	N
vg0142041116	G -> A	LOC_Os01g72500.1	upstream_gene_variant ; 10.0bp to feature; MODIFIER	silent_mutation	Average:51.596; most accessible tissue: Zhenshan97 panicle, score: 68.538	N	N	N	N
vg0142041116	G -> A	LOC_Os01g72490.2	upstream_gene_variant ; 2009.0bp to feature; MODIFIER	silent_mutation	Average:51.596; most accessible tissue: Zhenshan97 panicle, score: 68.538	N	N	N	N
vg0142041116	G -> A	LOC_Os01g72490-LOC_Os01g72500	intergenic_region ; MODIFIER	silent_mutation	Average:51.596; most accessible tissue: Zhenshan97 panicle, score: 68.538	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0142041116	4.90E-06	4.90E-06	mr1770	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