Search for Variation information by Variation ID:

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

Detailed information for vg1108752857:

Variant ID: vg1108752857 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 8752857
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTCTGATACTTTTAAATTGTGCTTGTTTTCTTTATCTTTGTCTGGTACTGCTTTTACATGGTTTACTTCTTTACCGGCAAATTCTATTCATACTTGGCCT[C/T]
AATTAGAGCAAAGATTTCATGATTATTTCTATACTGGTGAAATTGAACTTAGGCTATGATTTGACGTTGATTAAGCAAAAGTACAATGAATCTGTCATTA

Reverse complement sequence

TAATGACAGATTCATTGTACTTTTGCTTAATCAACGTCAAATCATAGCCTAAGTTCAATTTCACCAGTATAGAAATAATCATGAAATCTTTGCTCTAATT[G/A]
AGGCCAAGTATGAATAGAATTTGCCGGTAAAGAAGTAAACCATGTAAAAGCAGTACCAGACAAAGATAAAGAAAACAAGCACAATTTAAAAGTATCAGAA

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	94.20%	2.10%	3.45%	0.32%	NA
All Indica	2759	91.00%	3.30%	5.65%	0.07%	NA
All Japonica	1512	98.60%	0.10%	0.40%	0.86%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	98.30%	0.20%	1.34%	0.17%	NA
Indica II	465	84.70%	5.20%	9.89%	0.22%	NA
Indica III	913	89.50%	4.70%	5.81%	0.00%	NA
Indica Intermediate	786	91.00%	2.80%	6.23%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.40%	0.40%	0.20%	0.00%	NA
Japonica Intermediate	241	92.50%	0.00%	2.07%	5.39%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	94.40%	5.60%	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
vg1108752857	C -> T	LOC_Os11g15450.1	upstream_gene_variant ; 3527.0bp to feature; MODIFIER	silent_mutation	Average:27.788; most accessible tissue: Zhenshan97 root, score: 41.416	N	N	N	N
vg1108752857	C -> T	LOC_Os11g15440.1	intron_variant ; MODIFIER	silent_mutation	Average:27.788; most accessible tissue: Zhenshan97 root, score: 41.416	N	N	N	N
vg1108752857	C -> DEL	N	N	silent_mutation	Average:27.788; most accessible tissue: Zhenshan97 root, score: 41.416	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1108752857	8.71E-06	8.69E-06	mr1919_2	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
vg1108752857	4.03E-06	4.03E-06	mr1919_2	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