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Detailed information for vg1124210586:

Variant ID: vg1124210586 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 24210586
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.68, C: 0.32, others allele: 0.00, population size: 195. )

Flanking Sequence (100 bp) in Reference Genome:


TTGATGGGAATTGGACCTCTTAATTCCCTATCCCAAACCCTCTCGAATTCCCAAGTCTTTCAACCAAACTACAGATTTAAACTCCTAGATATCATAAACT[C/T]
CCATTCCTCATCACTAACTCCCTCCAACCAAACAAACCGTATGATCACATCAAAGTACAAAAAACATGTCTAAAAACAGTTTCTAATTATATGCTGTTCA

Reverse complement sequence

TGAACAGCATATAATTAGAAACTGTTTTTAGACATGTTTTTTGTACTTTGATGTGATCATACGGTTTGTTTGGTTGGAGGGAGTTAGTGATGAGGAATGG[G/A]
AGTTTATGATATCTAGGAGTTTAAATCTGTAGTTTGGTTGAAAGACTTGGGAATTCGAGAGGGTTTGGGATAGGGAATTAAGAGGTCCAATTCCCATCAA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 75.40% 24.10% 0.51% 0.00% NA
All Indica  2759 94.70% 4.90% 0.47% 0.00% NA
All Japonica  1512 52.10% 47.60% 0.33% 0.00% NA
Aus  269 25.30% 73.20% 1.49% 0.00% NA
Indica I  595 97.10% 2.70% 0.17% 0.00% NA
Indica II  465 96.30% 3.00% 0.65% 0.00% NA
Indica III  913 94.40% 4.90% 0.66% 0.00% NA
Indica Intermediate  786 92.10% 7.50% 0.38% 0.00% NA
Temperate Japonica  767 35.60% 63.80% 0.65% 0.00% NA
Tropical Japonica  504 66.30% 33.70% 0.00% 0.00% NA
Japonica Intermediate  241 75.10% 24.90% 0.00% 0.00% NA
VI/Aromatic  96 29.20% 70.80% 0.00% 0.00% NA
Intermediate  90 73.30% 24.40% 2.22% 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
vg1124210586 C -> T LOC_Os11g40564.1 upstream_gene_variant ; 1071.0bp to feature; MODIFIER silent_mutation Average:73.764; most accessible tissue: Zhenshan97 flower, score: 90.51 N N N N
vg1124210586 C -> T LOC_Os11g40570.1 downstream_gene_variant ; 89.0bp to feature; MODIFIER silent_mutation Average:73.764; most accessible tissue: Zhenshan97 flower, score: 90.51 N N N N
vg1124210586 C -> T LOC_Os11g40570.3 downstream_gene_variant ; 60.0bp to feature; MODIFIER silent_mutation Average:73.764; most accessible tissue: Zhenshan97 flower, score: 90.51 N N N N
vg1124210586 C -> T LOC_Os11g40570.2 downstream_gene_variant ; 60.0bp to feature; MODIFIER silent_mutation Average:73.764; most accessible tissue: Zhenshan97 flower, score: 90.51 N N N N
vg1124210586 C -> T LOC_Os11g40564-LOC_Os11g40570 intergenic_region ; MODIFIER silent_mutation Average:73.764; most accessible tissue: Zhenshan97 flower, score: 90.51 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)
vg1124210586 C T -0.03 -0.02 -0.01 -0.03 -0.02 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1124210586 NA 7.16E-09 mr1693_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