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Detailed information for vg1109226985:

Variant ID: vg1109226985 (JBrowse)Variation Type: INDEL
Chromosome: chr11Position: 9226985
Reference Allele: TAlternative Allele: A,TTA
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AAAATGATAAATAGTGTACTACTTATCATATGTTATAAAAAAAATTGGACATATCCTCCACATGTTATATAAAAAAAATTTGAACATACCCTCCCACATG[T/A,TTA]
TACACAAAAAAAAATGAACAAAAACCAACAATCACCCATTTTCATTCACATATCACCCACATTCCCACATTCACATTCACAATCAACATATGACCCCTCA

Reverse complement sequence

TGAGGGGTCATATGTTGATTGTGAATGTGAATGTGGGAATGTGGGTGATATGTGAATGAAAATGGGTGATTGTTGGTTTTTGTTCATTTTTTTTTGTGTA[A/T,TAA]
CATGTGGGAGGGTATGTTCAAATTTTTTTTATATAACATGTGGAGGATATGTCCAATTTTTTTTATAACATATGATAAGTAGTACACTATTTATCATTTT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 91.40% 6.40% 1.86% 0.00% TTA: 0.36%
All Indica  2759 99.50% 0.10% 0.04% 0.00% TTA: 0.43%
All Japonica  1512 75.00% 19.20% 5.49% 0.00% TTA: 0.33%
Aus  269 98.50% 0.70% 0.74% 0.00% NA
Indica I  595 99.80% 0.00% 0.00% 0.00% TTA: 0.17%
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.00% 0.20% 0.00% 0.00% TTA: 0.77%
Indica Intermediate  786 99.40% 0.00% 0.13% 0.00% TTA: 0.51%
Temperate Japonica  767 90.70% 2.30% 6.91% 0.00% NA
Tropical Japonica  504 45.60% 49.40% 3.97% 0.00% TTA: 0.99%
Japonica Intermediate  241 86.30% 9.50% 4.15% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 90.00% 7.80% 2.22% 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
vg1109226985 T -> TTA LOC_Os11g16630.1 upstream_gene_variant ; 231.0bp to feature; MODIFIER silent_mutation Average:41.741; most accessible tissue: Zhenshan97 young leaf, score: 73.147 N N N N
vg1109226985 T -> TTA LOC_Os11g16640.1 downstream_gene_variant ; 1371.0bp to feature; MODIFIER silent_mutation Average:41.741; most accessible tissue: Zhenshan97 young leaf, score: 73.147 N N N N
vg1109226985 T -> TTA LOC_Os11g16630-LOC_Os11g16640 intergenic_region ; MODIFIER silent_mutation Average:41.741; most accessible tissue: Zhenshan97 young leaf, score: 73.147 N N N N
vg1109226985 T -> A LOC_Os11g16630.1 upstream_gene_variant ; 230.0bp to feature; MODIFIER silent_mutation Average:41.741; most accessible tissue: Zhenshan97 young leaf, score: 73.147 N N N N
vg1109226985 T -> A LOC_Os11g16640.1 downstream_gene_variant ; 1372.0bp to feature; MODIFIER silent_mutation Average:41.741; most accessible tissue: Zhenshan97 young leaf, score: 73.147 N N N N
vg1109226985 T -> A LOC_Os11g16630-LOC_Os11g16640 intergenic_region ; MODIFIER silent_mutation Average:41.741; most accessible tissue: Zhenshan97 young leaf, score: 73.147 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1109226985 NA 6.03E-12 mr1016 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
vg1109226985 2.23E-06 NA mr1017 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
vg1109226985 NA 1.85E-12 mr1017 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
vg1109226985 1.38E-07 NA mr1018 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
vg1109226985 NA 6.77E-11 mr1018 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
vg1109226985 2.20E-06 NA mr1019 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
vg1109226985 NA 2.27E-09 mr1019 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
vg1109226985 4.98E-09 NA mr1055 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
vg1109226985 7.59E-06 9.89E-15 mr1055 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
vg1109226985 1.02E-07 NA mr1132 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
vg1109226985 NA 1.81E-13 mr1132 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
vg1109226985 NA 5.78E-10 mr1178 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
vg1109226985 NA 3.23E-11 mr1390 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
vg1109226985 NA 7.33E-12 mr1490 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
vg1109226985 1.26E-06 NA mr1019_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
vg1109226985 NA 1.04E-09 mr1019_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
vg1109226985 NA 1.69E-12 mr1055_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
vg1109226985 4.40E-07 NA mr1132_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
vg1109226985 NA 1.49E-14 mr1132_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
vg1109226985 NA 5.90E-14 mr1390_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
vg1109226985 2.81E-06 NA mr1490_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
vg1109226985 6.77E-06 3.15E-15 mr1490_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
vg1109226985 NA 3.97E-06 mr1498_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