Search for Variation information by Variation ID:

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

Detailed information for vg1117158706:

Variant ID: vg1117158706 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 17158706
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGAAGTCGAAGCTGCCGAATCGGAACGCCTGCCCGGGAGGGAAGGCGAAGTCGTCGATGCCAGAAACGAAACCCATCGTACTTAGTCGGCGAGAACTTGA[C/T]
GCCTCCCCTACCTGGCGAGCCAACTATCGAAACAAGATTTCGGCAATAATAAAAGGGGGTGGCTATCAAGCTAGGAAAGTGGATGGGTTTGGAGACAATG

Reverse complement sequence

CATTGTCTCCAAACCCATCCACTTTCCTAGCTTGATAGCCACCCCCTTTTATTATTGCCGAAATCTTGTTTCGATAGTTGGCTCGCCAGGTAGGGGAGGC[G/A]
TCAAGTTCTCGCCGACTAAGTACGATGGGTTTCGTTTCTGGCATCGACGACTTCGCCTTCCCTCCCGGGCAGGCGTTCCGATTCGGCAGCTTCGACTTCA

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	89.80%	0.60%	1.52%	8.15%	NA
All Indica	2759	99.10%	0.40%	0.33%	0.18%	NA
All Japonica	1512	72.90%	0.90%	3.90%	22.22%	NA
Aus	269	99.60%	0.00%	0.37%	0.00%	NA
Indica I	595	98.30%	0.30%	0.67%	0.67%	NA
Indica II	465	99.10%	0.20%	0.65%	0.00%	NA
Indica III	913	99.30%	0.50%	0.11%	0.00%	NA
Indica Intermediate	786	99.40%	0.40%	0.13%	0.13%	NA
Temperate Japonica	767	92.00%	0.40%	0.39%	7.17%	NA
Tropical Japonica	504	54.00%	2.20%	9.92%	33.93%	NA
Japonica Intermediate	241	51.90%	0.00%	2.49%	45.64%	NA
VI/Aromatic	96	53.10%	0.00%	2.08%	44.79%	NA
Intermediate	90	96.70%	1.10%	1.11%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1117158706	C -> T	LOC_Os11g29570.1	upstream_gene_variant ; 25.0bp to feature; MODIFIER	silent_mutation	Average:26.337; most accessible tissue: Minghui63 young leaf, score: 44.63	N	N	N	N
vg1117158706	C -> T	LOC_Os11g29580.1	downstream_gene_variant ; 4038.0bp to feature; MODIFIER	silent_mutation	Average:26.337; most accessible tissue: Minghui63 young leaf, score: 44.63	N	N	N	N
vg1117158706	C -> T	LOC_Os11g29570-LOC_Os11g29580	intergenic_region ; MODIFIER	silent_mutation	Average:26.337; most accessible tissue: Minghui63 young leaf, score: 44.63	N	N	N	N
vg1117158706	C -> DEL	N	N	silent_mutation	Average:26.337; most accessible tissue: Minghui63 young leaf, score: 44.63	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1117158706	NA	9.99E-06	mr1376	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
vg1117158706	NA	9.99E-06	mr1431	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
vg1117158706	NA	7.67E-07	mr1921	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