Search for Variation information by Variation ID:

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

Detailed information for vg0622637477:

Variant ID: vg0622637477 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 22637477
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTCTTTGATGGATCGGTCTGCACCCATGGTTGTGGCATCGGCTTGGTTATAATTTCCCCTAGGGGGCATGTTTTGAGTTTGCTTATACTATTAAACCATA[T/C]
GCAACTAATAATCAAGCTGAATATGAGGCAGTGCTCAAGAGGTTGCAGTTACTCAAGGAAGTTGAAGCCGATACTATTGAAATCATGGGGGATTCTTTGC

Reverse complement sequence

GCAAAGAATCCCCCATGATTTCAATAGTATCGGCTTCAACTTCCTTGAGTAACTGCAACCTCTTGAGCACTGCCTCATATTCAGCTTGATTATTAGTTGC[A/G]
TATGGTTTAATAGTATAAGCAAACTCAAAACATGCCCCCTAGGGGAAATTATAACCAAGCCGATGCCACAACCATGGGTGCAGACCGATCCATCAAAGAA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	92.80%	3.70%	2.81%	0.66%	NA
All Indica	2759	95.20%	2.00%	1.67%	1.12%	NA
All Japonica	1512	87.00%	7.60%	5.42%	0.00%	NA
Aus	269	99.30%	0.40%	0.37%	0.00%	NA
Indica I	595	96.10%	1.20%	0.67%	2.02%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	92.10%	3.50%	3.29%	1.10%	NA
Indica Intermediate	786	95.20%	2.20%	1.53%	1.15%	NA
Temperate Japonica	767	97.70%	1.60%	0.78%	0.00%	NA
Tropical Japonica	504	74.20%	14.90%	10.91%	0.00%	NA
Japonica Intermediate	241	79.70%	11.60%	8.71%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	91.10%	4.40%	4.44%	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
vg0622637477	T -> C	LOC_Os06g38250.1	upstream_gene_variant ; 4576.0bp to feature; MODIFIER	silent_mutation	Average:28.451; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N
vg0622637477	T -> C	LOC_Os06g38270.1	downstream_gene_variant ; 1971.0bp to feature; MODIFIER	silent_mutation	Average:28.451; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N
vg0622637477	T -> C	LOC_Os06g38260.1	intron_variant ; MODIFIER	silent_mutation	Average:28.451; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N
vg0622637477	T -> DEL	N	N	silent_mutation	Average:28.451; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0622637477	4.06E-06	4.06E-06	mr1184	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
vg0622637477	NA	3.09E-08	mr1951	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