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Detailed information for vg0129240128:

Variant ID: vg0129240128 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 29240128
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 345. )

Flanking Sequence (100 bp) in Reference Genome:


TTCTCAAGTACAAATCATGCAAGCGTGCTTCGAAACTTTTCGATGATCAAGCAGGAGTATAATATCTTGACTTTACTAGCTTGGCTTCTCAAAAGTTAGG[A/G]
TTCAGGATATGGTTGCCACCCAAAAGAGAAGCAAAATATAGTTGCTTAGACTCACCCTGGGTACTACTGTACTAGGTAGCCAAGTCCAAGGTAAATCAGT

Reverse complement sequence

ACTGATTTACCTTGGACTTGGCTACCTAGTACAGTAGTACCCAGGGTGAGTCTAAGCAACTATATTTTGCTTCTCTTTTGGGTGGCAACCATATCCTGAA[T/C]
CCTAACTTTTGAGAAGCCAAGCTAGTAAAGTCAAGATATTATACTCCTGCTTGATCATCGAAAAGTTTCGAAGCACGCTTGCATGATTTGTACTTGAGAA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 92.90% 7.00% 0.11% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 79.00% 20.70% 0.33% 0.00% NA
Aus  269 99.60% 0.40% 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 91.50% 8.10% 0.39% 0.00% NA
Tropical Japonica  504 72.40% 27.60% 0.00% 0.00% NA
Japonica Intermediate  241 52.70% 46.50% 0.83% 0.00% NA
VI/Aromatic  96 90.60% 9.40% 0.00% 0.00% NA
Intermediate  90 93.30% 6.70% 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
vg0129240128 A -> G LOC_Os01g50930.1 3_prime_UTR_variant ; 4013.0bp to feature; MODIFIER silent_mutation Average:83.371; most accessible tissue: Zhenshan97 panicle, score: 92.133 N N N N
vg0129240128 A -> G LOC_Os01g50930.2 3_prime_UTR_variant ; 309.0bp to feature; MODIFIER silent_mutation Average:83.371; most accessible tissue: Zhenshan97 panicle, score: 92.133 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)
vg0129240128 A G 0.03 0.01 0.01 0.01 -0.01 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0129240128 3.61E-06 NA mr1534 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
vg0129240128 NA 4.25E-06 mr1534 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
vg0129240128 NA 4.24E-09 mr1693 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
vg0129240128 NA 3.97E-06 mr1064_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
vg0129240128 NA 9.75E-07 mr1691_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
vg0129240128 6.20E-06 NA mr1768_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