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Detailed information for vg1105811378:

Variant ID: vg1105811378 (JBrowse)Variation Type: INDEL
Chromosome: chr11Position: 5811378
Reference Allele: CTAAlternative Allele: TTA,C
Primary Allele: CTASecondary Allele: TTA

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CATCTTAATCAATAAATAAAGAATTTATTCTATTTTTTATACAATAAAGCAATAGTAATTAAAAAATTAATATAAAAACAAACAACAATTAGCTAAATGA[CTA/TTA,C]
TATCATAAGTTACTTCTGGTTTTTAAGTTCATTTGAACTATCATTTTATTTATAAATAAATAAATAATTTAATATCCATATTACCCATTTTTCACTGTAA

Reverse complement sequence

TTACAGTGAAAAATGGGTAATATGGATATTAAATTATTTATTTATTTATAAATAAAATGATAGTTCAAATGAACTTAAAAACCAGAAGTAACTTATGATA[TAG/TAA,G]
TCATTTAGCTAATTGTTGTTTGTTTTTATATTAATTTTTTAATTACTATTGCTTTATTGTATAAAAAATAGAATAAATTCTTTATTTATTGATTAAGATG

Allele Frequencies:

Populations Population SizeFrequency of CTA(primary allele) Frequency of TTA(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 54.60% 28.20% 4.89% 7.02% C: 5.25%
All Indica  2759 41.80% 36.30% 6.31% 7.03% C: 8.59%
All Japonica  1512 85.30% 9.90% 2.12% 2.58% C: 0.20%
Aus  269 6.30% 55.80% 1.12% 35.32% C: 1.49%
Indica I  595 22.20% 69.10% 4.20% 3.87% C: 0.67%
Indica II  465 67.30% 9.70% 4.30% 1.72% C: 16.99%
Indica III  913 38.90% 27.90% 9.86% 14.35% C: 8.98%
Indica Intermediate  786 44.80% 37.00% 4.96% 4.07% C: 9.16%
Temperate Japonica  767 92.70% 1.80% 2.48% 2.61% C: 0.39%
Tropical Japonica  504 76.40% 18.50% 1.39% 3.77% NA
Japonica Intermediate  241 80.10% 17.40% 2.49% 0.00% NA
VI/Aromatic  96 74.00% 9.40% 15.62% 0.00% C: 1.04%
Intermediate  90 58.90% 25.60% 7.78% 4.44% C: 3.33%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1105811378 CTA -> TTA LOC_Os11g10600.1 upstream_gene_variant ; 1907.0bp to feature; MODIFIER silent_mutation Average:37.06; most accessible tissue: Minghui63 flag leaf, score: 73.334 N N N N
vg1105811378 CTA -> TTA LOC_Os11g10590.1 downstream_gene_variant ; 2361.0bp to feature; MODIFIER silent_mutation Average:37.06; most accessible tissue: Minghui63 flag leaf, score: 73.334 N N N N
vg1105811378 CTA -> TTA LOC_Os11g10590-LOC_Os11g10600 intergenic_region ; MODIFIER silent_mutation Average:37.06; most accessible tissue: Minghui63 flag leaf, score: 73.334 N N N N
vg1105811378 CTA -> DEL N N silent_mutation Average:37.06; most accessible tissue: Minghui63 flag leaf, score: 73.334 N N N N
vg1105811378 CTA -> C LOC_Os11g10600.1 upstream_gene_variant ; 1906.0bp to feature; MODIFIER silent_mutation Average:37.06; most accessible tissue: Minghui63 flag leaf, score: 73.334 N N N N
vg1105811378 CTA -> C LOC_Os11g10590.1 downstream_gene_variant ; 2362.0bp to feature; MODIFIER silent_mutation Average:37.06; most accessible tissue: Minghui63 flag leaf, score: 73.334 N N N N
vg1105811378 CTA -> C LOC_Os11g10590-LOC_Os11g10600 intergenic_region ; MODIFIER silent_mutation Average:37.06; most accessible tissue: Minghui63 flag leaf, score: 73.334 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1105811378 7.23E-07 7.23E-07 mr1460_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
vg1105811378 NA 4.97E-06 mr1928_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
vg1105811378 NA 3.19E-06 mr1931_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