Search for Variation information by Variation ID:

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

Detailed information for vg0142527699:

Variant ID: vg0142527699 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 42527699
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATATCTGGGGTGAGGTTACAACGCCGCACGACGGCTTACAAGAGGTATATATATGGTAGAACCCTAAAAGGGATGACGATCCGTTTCGCCCAAGCCTCCC[G/A]
GCGACGGGCCTCCGCTCCACTACGGCAGAAGCTGGCCTTTATTAAGTGCAAATGAATTTGGATCACAACTCAACAAACTCCACCTTGAGACAAATTCCTT

Reverse complement sequence

AAGGAATTTGTCTCAAGGTGGAGTTTGTTGAGTTGTGATCCAAATTCATTTGCACTTAATAAAGGCCAGCTTCTGCCGTAGTGGAGCGGAGGCCCGTCGC[C/T]
GGGAGGCTTGGGCGAAACGGATCGTCATCCCTTTTAGGGTTCTACCATATATATACCTCTTGTAAGCCGTCGTGCGGCGTTGTAACCTCACCCCAGATAT

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	96.80%	0.60%	0.74%	1.86%	NA
All Indica	2759	99.90%	0.00%	0.04%	0.07%	NA
All Japonica	1512	90.40%	1.90%	2.18%	5.49%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.60%	0.00%	0.00%	0.43%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	99.90%	0.00%	0.13%	0.00%	NA
Temperate Japonica	767	98.20%	1.00%	0.39%	0.39%	NA
Tropical Japonica	504	76.80%	3.00%	5.16%	15.08%	NA
Japonica Intermediate	241	94.20%	2.50%	1.66%	1.66%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	95.60%	0.00%	1.11%	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
vg0142527699	G -> A	LOC_Os01g73370.1	upstream_gene_variant ; 318.0bp to feature; MODIFIER	silent_mutation	Average:46.299; most accessible tissue: Zhenshan97 panicle, score: 68.538	N	N	N	N
vg0142527699	G -> A	LOC_Os01g73380.1	downstream_gene_variant ; 178.0bp to feature; MODIFIER	silent_mutation	Average:46.299; most accessible tissue: Zhenshan97 panicle, score: 68.538	N	N	N	N
vg0142527699	G -> A	LOC_Os01g73390.1	downstream_gene_variant ; 4552.0bp to feature; MODIFIER	silent_mutation	Average:46.299; most accessible tissue: Zhenshan97 panicle, score: 68.538	N	N	N	N
vg0142527699	G -> A	LOC_Os01g73370-LOC_Os01g73380	intergenic_region ; MODIFIER	silent_mutation	Average:46.299; most accessible tissue: Zhenshan97 panicle, score: 68.538	N	N	N	N
vg0142527699	G -> DEL	N	N	silent_mutation	Average:46.299; 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
vg0142527699	2.52E-06	5.93E-07	mr1519_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