Search for Variation information by Variation ID:

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

Detailed information for vg0130302150:

Variant ID: vg0130302150 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 30302150
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TATATACTAAAAGTCCATTAAACTTCCTACAAACGCTCCTAAGCCGCCACATGGCGCTCCTACAAACACTCCTAAACCGCCACGTGGCACTATCTAATCT[C/T]
ATTGTTGATTTTCACTTAGATTGGTGCACCGTTAATTTAGACCATTAGATTAGATCTATTATTAAAAAGGTGATAGTTTTTCTAAAAAAATATGCAACTG

Reverse complement sequence

CAGTTGCATATTTTTTTAGAAAAACTATCACCTTTTTAATAATAGATCTAATCTAATGGTCTAAATTAACGGTGCACCAATCTAAGTGAAAATCAACAAT[G/A]
AGATTAGATAGTGCCACGTGGCGGTTTAGGAGTGTTTGTAGGAGCGCCATGTGGCGGCTTAGGAGCGTTTGTAGGAAGTTTAATGGACTTTTAGTATATA

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	96.70%	1.90%	0.49%	0.89%	NA
All Indica	2759	96.10%	3.30%	0.65%	0.00%	NA
All Japonica	1512	97.00%	0.00%	0.20%	2.78%	NA
Aus	269	99.60%	0.00%	0.37%	0.00%	NA
Indica I	595	96.50%	3.40%	0.17%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	94.00%	4.30%	1.75%	0.00%	NA
Indica Intermediate	786	95.90%	3.90%	0.13%	0.00%	NA
Temperate Japonica	767	98.20%	0.00%	0.00%	1.83%	NA
Tropical Japonica	504	98.20%	0.00%	0.40%	1.39%	NA
Japonica Intermediate	241	90.90%	0.00%	0.41%	8.71%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	1.10%	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
vg0130302150	C -> T	LOC_Os01g52700.1	downstream_gene_variant ; 2201.0bp to feature; MODIFIER	silent_mutation	Average:43.188; most accessible tissue: Zhenshan97 panicle, score: 71.253	N	N	N	N
vg0130302150	C -> T	LOC_Os01g52690-LOC_Os01g52700	intergenic_region ; MODIFIER	silent_mutation	Average:43.188; most accessible tissue: Zhenshan97 panicle, score: 71.253	N	N	N	N
vg0130302150	C -> DEL	N	N	silent_mutation	Average:43.188; most accessible tissue: Zhenshan97 panicle, score: 71.253	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0130302150	1.37E-06	1.37E-06	mr1459	Ind_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
vg0130302150	NA	8.07E-06	mr1364_2	Ind_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