Search for Variation information by Variation ID:

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

Detailed information for vg1106408812:

Variant ID: vg1106408812 (JBrowse)Variation Type: INDEL
Chromosome: chr11Position: 6408812
Reference Allele: CACTAlternative Allele: TACT,C
Primary Allele: CACTSecondary Allele: TACT

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGCCTTCGACACCTATAAAAACCAGCGAGCTCCTCCATTTTTTCCCATCCAAATCTGAGCTCCATTTTTGCTCTCTCTCTCTCTCTCTCCAATCCTCCCC[CACT/TACT,C]
GGCCGCCATTCACTTTGCTCCTCCGCCGGCTGCTGTTCTTGGCTCCTCCACCGTCGGCCGCCCTAGCGCCGCCTTTGGCTGCCGCCGCCGTCAGGCACCA

Reverse complement sequence

TGGTGCCTGACGGCGGCGGCAGCCAAAGGCGGCGCTAGGGCGGCCGACGGTGGAGGAGCCAAGAACAGCAGCCGGCGGAGGAGCAAAGTGAATGGCGGCC[AGTG/AGTA,G]
GGGGAGGATTGGAGAGAGAGAGAGAGAGAGCAAAAATGGAGCTCAGATTTGGATGGGAAAAAATGGAGGAGCTCGCTGGTTTTTATAGGTGTCGAAGGCG

Allele Frequencies:

Populations Population SizeFrequency of CACT(primary allele) Frequency of TACT(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 58.20% 41.40% 0.44% 0.00% C: 0.02%
All Indica  2759 39.00% 60.30% 0.65% 0.00% C: 0.04%
All Japonica  1512 93.80% 6.00% 0.20% 0.00% NA
Aus  269 38.70% 61.30% 0.00% 0.00% NA
Indica I  595 31.30% 67.20% 1.51% 0.00% NA
Indica II  465 21.30% 77.80% 0.86% 0.00% NA
Indica III  913 56.60% 43.30% 0.00% 0.00% C: 0.11%
Indica Intermediate  786 35.00% 64.40% 0.64% 0.00% NA
Temperate Japonica  767 96.10% 3.70% 0.26% 0.00% NA
Tropical Japonica  504 90.90% 8.90% 0.20% 0.00% NA
Japonica Intermediate  241 92.50% 7.50% 0.00% 0.00% NA
VI/Aromatic  96 93.80% 6.20% 0.00% 0.00% NA
Intermediate  90 66.70% 33.30% 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
vg1106408812 CACT -> C LOC_Os11g11520.1 upstream_gene_variant ; 2155.0bp to feature; MODIFIER N Average:71.583; most accessible tissue: Zhenshan97 young leaf, score: 79.225 N N N N
vg1106408812 CACT -> C LOC_Os11g11530.1 upstream_gene_variant ; 2024.0bp to feature; MODIFIER N Average:71.583; most accessible tissue: Zhenshan97 young leaf, score: 79.225 N N N N
vg1106408812 CACT -> C LOC_Os11g11520-LOC_Os11g11530 intergenic_region ; MODIFIER N Average:71.583; most accessible tissue: Zhenshan97 young leaf, score: 79.225 N N N N
vg1106408812 CACT -> TACT LOC_Os11g11520.1 upstream_gene_variant ; 2154.0bp to feature; MODIFIER silent_mutation Average:71.583; most accessible tissue: Zhenshan97 young leaf, score: 79.225 N N N N
vg1106408812 CACT -> TACT LOC_Os11g11530.1 upstream_gene_variant ; 2025.0bp to feature; MODIFIER silent_mutation Average:71.583; most accessible tissue: Zhenshan97 young leaf, score: 79.225 N N N N
vg1106408812 CACT -> TACT LOC_Os11g11520-LOC_Os11g11530 intergenic_region ; MODIFIER silent_mutation Average:71.583; most accessible tissue: Zhenshan97 young leaf, score: 79.225 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1106408812 NA 3.09E-06 mr1224 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
vg1106408812 NA 9.06E-06 mr1277 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
vg1106408812 NA 6.65E-08 mr1335_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