Search for Variation information by Variation ID:

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

Detailed information for vg0511085884:

Variant ID: vg0511085884 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 11085884
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAATCATATGGATAAAAGACTTGATAGTGGTTCAAGGTATCACAAATGTCAAATTATTCGGTTCAAATTAAGTGAAAATTAGTTTAAAGGTGATGCAAAG[C/T]
GAACATTGATAATAAAGAGTAGCCTAAAGTGAAATTCACTCTTACAAATTATACTTGATTTTAATTTCAACAACTTATTTTTCGTTATTTTTGTTAATAC

Reverse complement sequence

GTATTAACAAAAATAACGAAAAATAAGTTGTTGAAATTAAAATCAAGTATAATTTGTAAGAGTGAATTTCACTTTAGGCTACTCTTTATTATCAATGTTC[G/A]
CTTTGCATCACCTTTAAACTAATTTTCACTTAATTTGAACCGAATAATTTGACATTTGTGATACCTTGAACCACTATCAAGTCTTTTATCCATATGATTT

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	97.40%	1.10%	1.48%	0.00%	NA
All Indica	2759	98.70%	0.00%	1.30%	0.00%	NA
All Japonica	1512	94.50%	3.30%	2.18%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	97.10%	0.00%	2.86%	0.00%	NA
Indica II	465	98.70%	0.00%	1.29%	0.00%	NA
Indica III	913	99.90%	0.00%	0.11%	0.00%	NA
Indica Intermediate	786	98.50%	0.00%	1.53%	0.00%	NA
Temperate Japonica	767	94.00%	2.10%	3.91%	0.00%	NA
Tropical Japonica	504	93.80%	6.00%	0.20%	0.00%	NA
Japonica Intermediate	241	97.50%	1.70%	0.83%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	96.70%	2.20%	1.11%	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
vg0511085884	C -> T	LOC_Os05g19100.1	upstream_gene_variant ; 2791.0bp to feature; MODIFIER	silent_mutation	Average:55.832; most accessible tissue: Minghui63 panicle, score: 79.811	N	N	N	N
vg0511085884	C -> T	LOC_Os05g19110.1	upstream_gene_variant ; 1776.0bp to feature; MODIFIER	silent_mutation	Average:55.832; most accessible tissue: Minghui63 panicle, score: 79.811	N	N	N	N
vg0511085884	C -> T	LOC_Os05g19100-LOC_Os05g19110	intergenic_region ; MODIFIER	silent_mutation	Average:55.832; most accessible tissue: Minghui63 panicle, score: 79.811	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0511085884	1.12E-07	1.12E-07	mr1173_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