Search for Variation information by Variation ID:

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

Detailed information for vg0602650491:

Variant ID: vg0602650491 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 2650491
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCTCATTGTCAATGTGTAGGTTTTGCCCAGTTTGATACGACATAGGCCGCCCACTTCTCCCAGGCTGCAGGGTCAGCGTCTCAGGTAGCTACGTCGGCCT[C/T]
GCACTATACGTAGTTCTGGCGGTACGCTGGGGCTTCGTCACAGGCAGCCGGCACGTCGAGTCGGGGTCCACCACTGGACCATGCCGGGACCTCGTCGGAG

Reverse complement sequence

CTCCGACGAGGTCCCGGCATGGTCCAGTGGTGGACCCCGACTCGACGTGCCGGCTGCCTGTGACGAAGCCCCAGCGTACCGCCAGAACTACGTATAGTGC[G/A]
AGGCCGACGTAGCTACCTGAGACGCTGACCCTGCAGCCTGGGAGAAGTGGGCGGCCTATGTCGTATCAAACTGGGCAAAACCTACACATTGACAATGAGA

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	99.10%	0.30%	0.59%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	97.20%	1.00%	1.85%	0.00%	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	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	94.90%	2.00%	3.13%	0.00%	NA
Tropical Japonica	504	99.40%	0.00%	0.60%	0.00%	NA
Japonica Intermediate	241	99.60%	0.00%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	100.00%	0.00%	0.00%	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
vg0602650491	C -> T	LOC_Os06g05820.1	upstream_gene_variant ; 1578.0bp to feature; MODIFIER	silent_mutation	Average:77.526; most accessible tissue: Zhenshan97 panicle, score: 86.058	N	N	N	N
vg0602650491	C -> T	LOC_Os06g05810.1	downstream_gene_variant ; 3914.0bp to feature; MODIFIER	silent_mutation	Average:77.526; most accessible tissue: Zhenshan97 panicle, score: 86.058	N	N	N	N
vg0602650491	C -> T	LOC_Os06g05810-LOC_Os06g05820	intergenic_region ; MODIFIER	silent_mutation	Average:77.526; most accessible tissue: Zhenshan97 panicle, score: 86.058	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0602650491	4.58E-06	2.27E-07	mr1201	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
vg0602650491	NA	5.61E-06	mr1201_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