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Detailed information for vg0333362258:

Variant ID: vg0333362258 (JBrowse)Variation Type: INDEL
Chromosome: chr03Position: 33362258
Reference Allele: ACTGTAAGAAGTTGGGTGATTAAGGCAlternative Allele: A
Primary Allele: ACTGTAAGAAGTTGGGTGAT TAAGGCSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AAGAATCTACTACTAGTGGAGTAAACAAGATTAGGCAGCAGCTCTGTGCTTGTACCCATTACAAGCAACAGTAAGCTGCAAGCTAGAGTAAAATACTGTC[ACTGTAAGAAGTTGGGTGATTAAGGC/A]
CCTGTTTAGATGGGACTAAAAGTTTTAAGTCCCTATCACATCGGATGTTTGAAAATTAATTATAAATATTAAACGTAGACTATTAATAAAACCCATCCAT

Reverse complement sequence

ATGGATGGGTTTTATTAATAGTCTACGTTTAATATTTATAATTAATTTTCAAACATCCGATGTGATAGGGACTTAAAACTTTTAGTCCCATCTAAACAGG[GCCTTAATCACCCAACTTCTTACAGT/T]
GACAGTATTTTACTCTAGCTTGCAGCTTACTGTTGCTTGTAATGGGTACAAGCACAGAGCTGCTGCCTAATCTTGTTTACTCCACTAGTAGTAGATTCTT

Allele Frequencies:

Populations Population SizeFrequency of ACTGTAAGAAGTTGGGTGAT TAAGGC(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.80% 0.30% 1.04% 3.91% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 84.00% 0.80% 3.17% 12.04% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 74.80% 1.40% 5.35% 18.38% NA
Tropical Japonica  504 95.20% 0.00% 0.99% 3.77% NA
Japonica Intermediate  241 89.60% 0.40% 0.83% 9.13% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 95.60% 0.00% 1.11% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0333362258 ACTGTAAGAAGTTGGGTGATTAAGGC -> A LOC_Os03g58580.1 3_prime_UTR_variant ; 245.0bp to feature; MODIFIER silent_mutation Average:89.477; most accessible tissue: Minghui63 young leaf, score: 97.588 N N N N
vg0333362258 ACTGTAAGAAGTTGGGTGATTAAGGC -> A LOC_Os03g58590.1 upstream_gene_variant ; 1727.0bp to feature; MODIFIER silent_mutation Average:89.477; most accessible tissue: Minghui63 young leaf, score: 97.588 N N N N
vg0333362258 ACTGTAAGAAGTTGGGTGATTAAGGC -> DEL N N silent_mutation Average:89.477; most accessible tissue: Minghui63 young leaf, score: 97.588 N N N N

Effects Predicted by Deep Convolutional Neural Networks

For each variant, we constructed two sequences that contain the variation site and the sequence around it, differing only in the variation site. We then used Basenji to predict the chromatin accessibility of each tissue for the two sequences, respectively, and scored the effect of the variant by comparing the changes in chromatin accessibility corresponding to the two genotypes in the 1 kb region around the variation site. The effect score was defined as the logarithmic ratio of the predicted chromatin accessibility of the alternative genotype to the value of the reference genotype.

Var ID Ref Alt Root (RT) Young Leaf (YL) Flag Leaf (FL) Young Panicle (YP) Lemma & Palea (LP) Stamen & Pistil (SP)
vg0333362258 ACTGT* A 0.4 -0.01 0.08 -0.18 -0.02 0.14

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0333362258 4.42E-06 NA mr1549 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