Search for Variation information by Variation ID:

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

Detailed information for vg0706508455:

Variant ID: vg0706508455 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 6508455
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTGAAACTTGAGCGTACCAGCACTAGTACAGATCCTTCTATCTGTGATGGCCTCTAACATGCCTGGAAATAGCGGGCCGTCACAAGGAAGTCATCTCAAT[C/T]
GGGCCAAAAAAGTGCCCGATTGAGATATGGTCGCATAGACATATTAGATGGGCATAAAACTTAAGCCCGTCACGGATGACACCTATTAATGACGGGCTGT

Reverse complement sequence

ACAGCCCGTCATTAATAGGTGTCATCCGTGACGGGCTTAAGTTTTATGCCCATCTAATATGTCTATGCGACCATATCTCAATCGGGCACTTTTTTGGCCC[G/A]
ATTGAGATGACTTCCTTGTGACGGCCCGCTATTTCCAGGCATGTTAGAGGCCATCACAGATAGAAGGATCTGTACTAGTGCTGGTACGCTCAAGTTTCAC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	83.70%	10.20%	4.55%	1.63%	NA
All Indica	2759	93.30%	0.50%	5.33%	0.87%	NA
All Japonica	1512	69.90%	25.00%	1.79%	3.31%	NA
Aus	269	62.10%	25.30%	12.64%	0.00%	NA
Indica I	595	88.10%	0.00%	10.25%	1.68%	NA
Indica II	465	94.60%	1.30%	3.66%	0.43%	NA
Indica III	913	96.70%	0.20%	2.30%	0.77%	NA
Indica Intermediate	786	92.40%	0.90%	6.11%	0.64%	NA
Temperate Japonica	767	90.90%	0.80%	1.83%	6.52%	NA
Tropical Japonica	504	26.80%	71.60%	1.59%	0.00%	NA
Japonica Intermediate	241	93.40%	4.60%	2.07%	0.00%	NA
VI/Aromatic	96	95.80%	4.20%	0.00%	0.00%	NA
Intermediate	90	72.20%	16.70%	7.78%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0706508455	C -> DEL	N	N	silent_mutation	Average:12.838; most accessible tissue: Callus, score: 46.613	N	N	N	N
vg0706508455	C -> T	LOC_Os07g11780.1	upstream_gene_variant ; 3021.0bp to feature; MODIFIER	silent_mutation	Average:12.838; most accessible tissue: Callus, score: 46.613	N	N	N	N
vg0706508455	C -> T	LOC_Os07g11770.1	downstream_gene_variant ; 1329.0bp to feature; MODIFIER	silent_mutation	Average:12.838; most accessible tissue: Callus, score: 46.613	N	N	N	N
vg0706508455	C -> T	LOC_Os07g11770-LOC_Os07g11780	intergenic_region ; MODIFIER	silent_mutation	Average:12.838; most accessible tissue: Callus, score: 46.613	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0706508455	NA	5.06E-06	mr1217_2	Jap_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
vg0706508455	NA	1.32E-08	mr1304_2	Jap_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
vg0706508455	4.86E-06	2.46E-08	mr1707_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