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Detailed information for vg0111809299:

Variant ID: vg0111809299 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 11809299
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.85, T: 0.15, others allele: 0.00, population size: 72. )

Flanking Sequence (100 bp) in Reference Genome:


CCGTGCTCCGTACTCTTTGTTTAGGTTTAATTTTATTGGTTTAGACTTTTAGTGGCTTTAGAGCATTAAATTTAATGGTGAAGAAGTCACACTCCTACTT[C/T]
AAATAAGTCAAAAATAGGTTGTTCAACTCAACTTTTGATTTAAGAGTGTAATAGTAGTTTTTGGCTTTAAAAAACTAAACAGAAAAACTTGTTCGTTCGT

Reverse complement sequence

ACGAACGAACAAGTTTTTCTGTTTAGTTTTTTAAAGCCAAAAACTACTATTACACTCTTAAATCAAAAGTTGAGTTGAACAACCTATTTTTGACTTATTT[G/A]
AAGTAGGAGTGTGACTTCTTCACCATTAAATTTAATGCTCTAAAGCCACTAAAAGTCTAAACCAATAAAATTAAACCTAAACAAAGAGTACGGAGCACGG

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 82.40% 17.50% 0.17% 0.00% NA
All Indica  2759 88.20% 11.70% 0.11% 0.00% NA
All Japonica  1512 68.20% 31.50% 0.26% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 88.10% 11.90% 0.00% 0.00% NA
Indica II  465 95.30% 4.70% 0.00% 0.00% NA
Indica III  913 88.80% 11.10% 0.11% 0.00% NA
Indica Intermediate  786 83.50% 16.30% 0.25% 0.00% NA
Temperate Japonica  767 72.20% 27.40% 0.39% 0.00% NA
Tropical Japonica  504 57.90% 41.90% 0.20% 0.00% NA
Japonica Intermediate  241 76.80% 23.20% 0.00% 0.00% NA
VI/Aromatic  96 85.40% 14.60% 0.00% 0.00% NA
Intermediate  90 86.70% 12.20% 1.11% 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
vg0111809299 C -> T LOC_Os01g21160.1 upstream_gene_variant ; 238.0bp to feature; MODIFIER silent_mutation Average:92.731; most accessible tissue: Callus, score: 97.125 N N N N
vg0111809299 C -> T LOC_Os01g21170.1 upstream_gene_variant ; 1386.0bp to feature; MODIFIER silent_mutation Average:92.731; most accessible tissue: Callus, score: 97.125 N N N N
vg0111809299 C -> T LOC_Os01g21160.2 upstream_gene_variant ; 750.0bp to feature; MODIFIER silent_mutation Average:92.731; most accessible tissue: Callus, score: 97.125 N N N N
vg0111809299 C -> T LOC_Os01g21160.4 upstream_gene_variant ; 265.0bp to feature; MODIFIER silent_mutation Average:92.731; most accessible tissue: Callus, score: 97.125 N N N N
vg0111809299 C -> T LOC_Os01g21160.3 upstream_gene_variant ; 238.0bp to feature; MODIFIER silent_mutation Average:92.731; most accessible tissue: Callus, score: 97.125 N N N N
vg0111809299 C -> T LOC_Os01g21180.1 downstream_gene_variant ; 2879.0bp to feature; MODIFIER silent_mutation Average:92.731; most accessible tissue: Callus, score: 97.125 N N N N
vg0111809299 C -> T LOC_Os01g21180.2 downstream_gene_variant ; 2879.0bp to feature; MODIFIER silent_mutation Average:92.731; most accessible tissue: Callus, score: 97.125 N N N N
vg0111809299 C -> T LOC_Os01g21160-LOC_Os01g21170 intergenic_region ; MODIFIER silent_mutation Average:92.731; most accessible tissue: Callus, score: 97.125 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)
vg0111809299 C T 0.03 -0.01 -0.01 0.01 0.01 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0111809299 NA 3.64E-06 mr1296_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
vg0111809299 6.45E-08 6.46E-08 mr1400_2 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
vg0111809299 NA 7.00E-10 mr1709_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
vg0111809299 NA 3.15E-07 mr1968_2 Ind_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