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Detailed information for vg0522118727:

Variant ID: vg0522118727 (JBrowse)Variation Type: INDEL
Chromosome: chr05Position: 22118727
Reference Allele: TAAlternative Allele: AA,TAAA,TAA,T
Primary Allele: AASecondary Allele: TA

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGATGAAAAGGAGTATCTAATTTGTAGGAAATTGCCTCTTTGTAATTTTAAATATTACTTTTACTTAAAATTTGCTGGATAAAAGAACATAAGTTTTTTT[TA/AA,TAAA,TAA,T]
AAAAAAAATCGGCCAACGAGTTTGTGTGAAACCTAAGTACAAGCCCGAGTAGGTCGCCCACAACTGGGGACTTTACCAGTGCGCTAAAATTTTCAGTTTG

Reverse complement sequence

CAAACTGAAAATTTTAGCGCACTGGTAAAGTCCCCAGTTGTGGGCGACCTACTCGGGCTTGTACTTAGGTTTCACACAAACTCGTTGGCCGATTTTTTTT[TA/TT,TTTA,TTA,A]
AAAAAAACTTATGTTCTTTTATCCAGCAAATTTTAAGTAAAAGTAATATTTAAAATTACAAAGAGGCAATTTCCTACAAATTAGATACTCCTTTTCATCT

Allele Frequencies:

Populations Population SizeFrequency of AA(primary allele) Frequency of TA(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 62.40% 34.40% 2.24% 0.57% TAA: 0.23%; TAAA: 0.13%; T: 0.02%
All Indica  2759 94.90% 2.30% 1.23% 0.98% TAA: 0.33%; TAAA: 0.22%
All Japonica  1512 9.50% 85.90% 4.50% 0.00% TAA: 0.13%
Aus  269 50.90% 48.70% 0.00% 0.00% T: 0.37%
Indica I  595 92.60% 1.70% 3.19% 1.18% TAA: 0.84%; TAAA: 0.50%
Indica II  465 97.00% 1.70% 0.65% 0.43% TAA: 0.22%
Indica III  913 97.20% 0.90% 0.22% 1.53% TAAA: 0.22%
Indica Intermediate  786 92.90% 4.80% 1.27% 0.51% TAA: 0.38%; TAAA: 0.13%
Temperate Japonica  767 12.40% 80.40% 7.04% 0.00% TAA: 0.13%
Tropical Japonica  504 5.40% 93.10% 1.39% 0.00% TAA: 0.20%
Japonica Intermediate  241 8.70% 88.40% 2.90% 0.00% NA
VI/Aromatic  96 4.20% 95.80% 0.00% 0.00% NA
Intermediate  90 52.20% 43.30% 4.44% 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
vg0522118727 TA -> DEL N N silent_mutation Average:62.589; most accessible tissue: Callus, score: 92.093 N N N N
vg0522118727 TA -> TAAA LOC_Os05g37780.1 upstream_gene_variant ; 4113.0bp to feature; MODIFIER silent_mutation Average:62.589; most accessible tissue: Callus, score: 92.093 N N N N
vg0522118727 TA -> TAAA LOC_Os05g37770-LOC_Os05g37780 intergenic_region ; MODIFIER silent_mutation Average:62.589; most accessible tissue: Callus, score: 92.093 N N N N
vg0522118727 TA -> T LOC_Os05g37780.1 upstream_gene_variant ; 4114.0bp to feature; MODIFIER silent_mutation Average:62.589; most accessible tissue: Callus, score: 92.093 N N N N
vg0522118727 TA -> T LOC_Os05g37770-LOC_Os05g37780 intergenic_region ; MODIFIER silent_mutation Average:62.589; most accessible tissue: Callus, score: 92.093 N N N N
vg0522118727 TA -> AA LOC_Os05g37780.1 upstream_gene_variant ; 4115.0bp to feature; MODIFIER silent_mutation Average:62.589; most accessible tissue: Callus, score: 92.093 N N N N
vg0522118727 TA -> AA LOC_Os05g37770-LOC_Os05g37780 intergenic_region ; MODIFIER silent_mutation Average:62.589; most accessible tissue: Callus, score: 92.093 N N N N
vg0522118727 TA -> TAA LOC_Os05g37780.1 upstream_gene_variant ; 4113.0bp to feature; MODIFIER silent_mutation Average:62.589; most accessible tissue: Callus, score: 92.093 N N N N
vg0522118727 TA -> TAA LOC_Os05g37770-LOC_Os05g37780 intergenic_region ; MODIFIER silent_mutation Average:62.589; most accessible tissue: Callus, score: 92.093 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0522118727 8.41E-06 7.21E-09 mr1549 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
vg0522118727 1.78E-06 2.38E-09 mr1757 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
vg0522118727 NA 4.26E-07 mr1549_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
vg0522118727 NA 5.21E-06 mr1757_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