Search for Variation information by Variation ID:

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

Detailed information for vg1121939108:

Variant ID: vg1121939108 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 21939108
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CACGCAGCAAATATGCAAGTGCACAGGATAACAAAGGATGGCATAGTATAGTCCCATTTGCATAAACAACATTTAATAAATATTTTAGAATTTAATAAAA[C/T]
AGTTAAATGATAATTAAACAATATTAATTCAACGTTATACAACATACCCTGTTGCATAGGCCCAACCATTCTGAACAACCAATCCCGGCTGCACAGTTCT

Reverse complement sequence

AGAACTGTGCAGCCGGGATTGGTTGTTCAGAATGGTTGGGCCTATGCAACAGGGTATGTTGTATAACGTTGAATTAATATTGTTTAATTATCATTTAACT[G/A]
TTTTATTAAATTCTAAAATATTTATTAAATGTTGTTTATGCAAATGGGACTATACTATGCCATCCTTTGTTATCCTGTGCACTTGCATATTTGCTGCGTG

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	85.30%	10.00%	0.11%	4.61%	NA
All Indica	2759	94.80%	1.40%	0.07%	3.70%	NA
All Japonica	1512	70.60%	27.20%	0.07%	2.18%	NA
Aus	269	75.80%	1.10%	0.74%	22.30%	NA
Indica I	595	99.50%	0.30%	0.00%	0.17%	NA
Indica II	465	99.10%	0.40%	0.00%	0.43%	NA
Indica III	913	91.10%	1.60%	0.11%	7.12%	NA
Indica Intermediate	786	93.00%	2.50%	0.13%	4.33%	NA
Temperate Japonica	767	88.50%	11.30%	0.00%	0.13%	NA
Tropical Japonica	504	39.10%	55.80%	0.20%	4.96%	NA
Japonica Intermediate	241	79.30%	17.80%	0.00%	2.90%	NA
VI/Aromatic	96	75.00%	7.30%	0.00%	17.71%	NA
Intermediate	90	78.90%	14.40%	0.00%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1121939108	C -> T	LOC_Os11g37160.1	upstream_gene_variant ; 2062.0bp to feature; MODIFIER	silent_mutation	Average:30.926; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N
vg1121939108	C -> T	LOC_Os11g37160-LOC_Os11g37170	intergenic_region ; MODIFIER	silent_mutation	Average:30.926; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N
vg1121939108	C -> DEL	N	N	silent_mutation	Average:30.926; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1121939108	NA	1.66E-07	mr1338	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
vg1121939108	NA	2.82E-07	mr1629	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
vg1121939108	NA	7.06E-08	mr1671	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
vg1121939108	3.05E-06	NA	mr1679	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
vg1121939108	NA	8.96E-09	mr1679	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
vg1121939108	NA	4.58E-06	mr1780	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
vg1121939108	NA	2.94E-07	mr1982	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
vg1121939108	NA	1.87E-06	mr1991	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
vg1121939108	NA	2.21E-06	mr1369_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
vg1121939108	NA	5.01E-06	mr1397_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
vg1121939108	NA	1.64E-06	mr1488_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
vg1121939108	NA	3.01E-07	mr1668_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
vg1121939108	1.65E-06	1.64E-06	mr1760_2	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
vg1121939108	2.68E-06	2.67E-06	mr1760_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
vg1121939108	NA	6.23E-06	mr1779_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