Search for Variation information by Variation ID:

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

Detailed information for vg1105129212:

Variant ID: vg1105129212 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 5129212
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, G: 0.01, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:

TATTTTTGATTTTTTTCCCATTTGAAACTGCAAAAGCCTTTTCTTCTGGCCCGGTGCTCCATTTGCGAATTTTTTTTCATTTTTAAATTTTTATTTTTTA[A/G]
TATTTACAGAAATATTATACCATCTAAAATATTTACAAAAATGTCCCCTGCCGCCCAAGTGGAGAGCGGCAAGGTGTGCGCATTTTGCACTGAGATCCCT

Reverse complement sequence

AGGGATCTCAGTGCAAAATGCGCACACCTTGCCGCTCTCCACTTGGGCGGCAGGGGACATTTTTGTAAATATTTTAGATGGTATAATATTTCTGTAAATA[T/C]
TAAAAAATAAAAATTTAAAAATGAAAAAAAATTCGCAAATGGAGCACCGGGCCAGAAGAAAAGGCTTTTGCAGTTTCAAATGGGAAAAAAATCAAAAATA

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	26.10%	22.20%	0.11%	51.61%	NA
All Indica	2759	11.80%	8.10%	0.11%	80.03%	NA
All Japonica	1512	37.90%	53.40%	0.07%	8.66%	NA
Aus	269	78.10%	0.00%	0.00%	21.93%	NA
Indica I	595	32.60%	2.90%	0.17%	64.37%	NA
Indica II	465	3.00%	3.40%	0.22%	93.33%	NA
Indica III	913	2.70%	7.00%	0.00%	90.25%	NA
Indica Intermediate	786	11.70%	16.00%	0.13%	72.14%	NA
Temperate Japonica	767	43.50%	53.20%	0.00%	3.26%	NA
Tropical Japonica	504	18.10%	64.50%	0.00%	17.46%	NA
Japonica Intermediate	241	61.40%	30.70%	0.41%	7.47%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	35.60%	17.80%	1.11%	45.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1105129212	A -> DEL	N	N	silent_mutation	Average:45.55; most accessible tissue: Callus, score: 77.364	N	N	N	N
vg1105129212	A -> G	LOC_Os11g09580.1	upstream_gene_variant ; 1806.0bp to feature; MODIFIER	silent_mutation	Average:45.55; most accessible tissue: Callus, score: 77.364	N	N	N	N
vg1105129212	A -> G	LOC_Os11g09590.1	upstream_gene_variant ; 41.0bp to feature; MODIFIER	silent_mutation	Average:45.55; most accessible tissue: Callus, score: 77.364	N	N	N	N
vg1105129212	A -> G	LOC_Os11g09580-LOC_Os11g09590	intergenic_region ; MODIFIER	silent_mutation	Average:45.55; most accessible tissue: Callus, score: 77.364	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1105129212	2.55E-07	NA	mr1182_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
vg1105129212	9.36E-06	9.35E-06	mr1262_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
vg1105129212	NA	6.84E-10	mr1282_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
vg1105129212	NA	5.27E-06	mr1624_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
vg1105129212	2.08E-06	4.71E-07	mr1661_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
vg1105129212	NA	2.53E-06	mr1662_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
vg1105129212	NA	7.44E-08	mr1723_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
vg1105129212	NA	2.10E-06	mr1800_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