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Detailed information for vg1128351408:

Variant ID: vg1128351408 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 28351408
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.52, C: 0.48, others allele: 0.00, population size: 73. )

Flanking Sequence (100 bp) in Reference Genome:


CTTCAAAGGGTGTGACCTAACAAATTAGCATTCCACGAAGCGACAACGCAGCACGGAGCAGTGGCGGATCTATAAAATCGATTTGTTGGTGTCATAATAA[T/C]
GTATGTATCGGTATCATTGTATGCTAACTATGTTTAGATCATACTGTTATAATATATGGATAAACAATTTTGCTATAGGTTTTATCGAAAGTTGTCGGTG

Reverse complement sequence

CACCGACAACTTTCGATAAAACCTATAGCAAAATTGTTTATCCATATATTATAACAGTATGATCTAAACATAGTTAGCATACAATGATACCGATACATAC[A/G]
TTATTATGACACCAACAAATCGATTTTATAGATCCGCCACTGCTCCGTGCTGCGTTGTCGCTTCGTGGAATGCTAATTTGTTAGGTCACACCCTTTGAAG

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 26.10% 14.30% 0.91% 58.65% NA
All Indica  2759 25.30% 12.20% 1.01% 61.51% NA
All Japonica  1512 22.40% 20.40% 0.73% 56.42% NA
Aus  269 30.90% 5.20% 0.74% 63.20% NA
Indica I  595 28.40% 15.10% 0.50% 55.97% NA
Indica II  465 22.60% 1.90% 0.86% 74.62% NA
Indica III  913 25.30% 14.80% 0.99% 58.93% NA
Indica Intermediate  786 24.60% 13.00% 1.53% 60.94% NA
Temperate Japonica  767 14.20% 32.20% 0.91% 52.67% NA
Tropical Japonica  504 33.30% 6.00% 0.79% 59.92% NA
Japonica Intermediate  241 25.70% 13.30% 0.00% 61.00% NA
VI/Aromatic  96 84.40% 3.10% 0.00% 12.50% NA
Intermediate  90 36.70% 16.70% 2.22% 44.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1128351408 T -> DEL N N silent_mutation Average:46.652; most accessible tissue: Minghui63 root, score: 93.736 N N N N
vg1128351408 T -> C LOC_Os11g47130.1 downstream_gene_variant ; 3548.0bp to feature; MODIFIER silent_mutation Average:46.652; most accessible tissue: Minghui63 root, score: 93.736 N N N N
vg1128351408 T -> C LOC_Os11g47130-LOC_Os11g47140 intergenic_region ; MODIFIER silent_mutation Average:46.652; most accessible tissue: Minghui63 root, score: 93.736 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)
vg1128351408 T C 0.07 0.05 0.03 0.02 0.04 0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1128351408 2.73E-07 2.73E-07 mr1795 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
vg1128351408 NA 1.72E-06 mr1150_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