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Detailed information for vg0141155876:

Variant ID: vg0141155876 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 41155876
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGAAACGATAGGCAAATAAACATAAAAAACAATAGAGGAGAGAAAAAATCACTGACACCAGCCAATAAAATATCTTCACTGTATCGGGGTAAAGTTACAA[C/T]
ACCGAATGGCGGCTTATAAGAGGTATATACATGAAGGTGAAACCCTAAAGGATAACGATCCATACCGCGGGGGCGCTTCGCTCCAGCAGAAACTGATATT

Reverse complement sequence

AATATCAGTTTCTGCTGGAGCGAAGCGCCCCCGCGGTATGGATCGTTATCCTTTAGGGTTTCACCTTCATGTATATACCTCTTATAAGCCGCCATTCGGT[G/A]
TTGTAACTTTACCCCGATACAGTGAAGATATTTTATTGGCTGGTGTCAGTGATTTTTTCTCTCCTCTATTGTTTTTTATGTTTATTTGCCTATCGTTTCC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 90.50% 4.10% 0.19% 5.21% NA
All Indica  2759 90.90% 0.60% 0.25% 8.23% NA
All Japonica  1512 98.50% 0.30% 0.07% 1.12% NA
Aus  269 36.10% 63.90% 0.00% 0.00% NA
Indica I  595 79.80% 0.00% 0.67% 19.50% NA
Indica II  465 97.40% 0.20% 0.00% 2.37% NA
Indica III  913 97.90% 0.40% 0.11% 1.53% NA
Indica Intermediate  786 87.40% 1.40% 0.25% 10.94% NA
Temperate Japonica  767 99.30% 0.00% 0.00% 0.65% NA
Tropical Japonica  504 98.40% 0.00% 0.00% 1.59% NA
Japonica Intermediate  241 96.30% 1.70% 0.41% 1.66% NA
VI/Aromatic  96 97.90% 1.00% 1.04% 0.00% NA
Intermediate  90 97.80% 0.00% 0.00% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0141155876 C -> T LOC_Os01g71106.2 3_prime_UTR_variant ; 1226.0bp to feature; MODIFIER silent_mutation Average:86.416; most accessible tissue: Zhenshan97 panicle, score: 93.133 N N N N
vg0141155876 C -> T LOC_Os01g71100.1 upstream_gene_variant ; 1198.0bp to feature; MODIFIER silent_mutation Average:86.416; most accessible tissue: Zhenshan97 panicle, score: 93.133 N N N N
vg0141155876 C -> T LOC_Os01g71114.1 downstream_gene_variant ; 3431.0bp to feature; MODIFIER silent_mutation Average:86.416; most accessible tissue: Zhenshan97 panicle, score: 93.133 N N N N
vg0141155876 C -> DEL N N silent_mutation Average:86.416; most accessible tissue: Zhenshan97 panicle, score: 93.133 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)
vg0141155876 C T -0.01 -0.05 -0.07 0.01 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0141155876 NA 1.98E-06 mr1262 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
vg0141155876 NA 9.69E-42 mr1549 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
vg0141155876 NA 7.65E-49 mr1550 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
vg0141155876 NA 1.46E-42 mr1757 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
vg0141155876 NA 3.34E-06 mr1931 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
vg0141155876 1.47E-06 NA mr1134_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
vg0141155876 NA 2.41E-08 mr1510_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
vg0141155876 NA 4.50E-15 mr1530_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
vg0141155876 NA 4.22E-31 mr1549_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
vg0141155876 NA 2.09E-48 mr1550_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
vg0141155876 NA 8.72E-06 mr1740_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
vg0141155876 NA 3.85E-28 mr1757_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