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Detailed information for vg1127725153:

Variant ID: vg1127725153 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 27725153
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.97, C: 0.03, others allele: 0.00, population size: 62. )

Flanking Sequence (100 bp) in Reference Genome:


CTCTGCCCGGGGGCGACGCGGGCGGCGGAACAAGCCGCGCCACCCCGTCCCTCTCCTCCCCTCAACCACCTCGCCGCCGCCTGAGCCGCCTGAGCTGAGG[C/T]
GTGCTCGTAGTGGTCGATGCAGTCCTCGATGTCGTAGGAGAGCTCGCGCACCTCCTTCATCCAGCACCTCACCACCATGGCCTGAGCCGGCTTTGCCGGC

Reverse complement sequence

GCCGGCAAAGCCGGCTCAGGCCATGGTGGTGAGGTGCTGGATGAAGGAGGTGCGCGAGCTCTCCTACGACATCGAGGACTGCATCGACCACTACGAGCAC[G/A]
CCTCAGCTCAGGCGGCTCAGGCGGCGGCGAGGTGGTTGAGGGGAGGAGAGGGACGGGGTGGCGCGGCTTGTTCCGCCGCCCGCGTCGCCCCCGGGCAGAG

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 43.20% 15.20% 0.93% 40.65% NA
All Indica  2759 50.30% 15.10% 0.80% 33.78% NA
All Japonica  1512 37.70% 16.70% 0.79% 44.78% NA
Aus  269 11.20% 8.60% 2.23% 78.07% NA
Indica I  595 37.10% 22.00% 1.68% 39.16% NA
Indica II  465 50.80% 14.00% 0.43% 34.84% NA
Indica III  913 61.10% 9.50% 0.00% 29.35% NA
Indica Intermediate  786 47.60% 16.90% 1.27% 34.22% NA
Temperate Japonica  767 32.60% 20.50% 0.91% 46.02% NA
Tropical Japonica  504 49.00% 5.60% 0.00% 45.44% NA
Japonica Intermediate  241 30.30% 28.20% 2.07% 39.42% NA
VI/Aromatic  96 15.60% 0.00% 3.12% 81.25% NA
Intermediate  90 41.10% 31.10% 1.11% 26.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1127725153 C -> T LOC_Os11g45809.1 downstream_gene_variant ; 4053.0bp to feature; MODIFIER silent_mutation Average:54.725; most accessible tissue: Minghui63 panicle, score: 98.135 N N N N
vg1127725153 C -> T LOC_Os11g45820.1 intron_variant ; MODIFIER silent_mutation Average:54.725; most accessible tissue: Minghui63 panicle, score: 98.135 N N N N
vg1127725153 C -> DEL N N silent_mutation Average:54.725; most accessible tissue: Minghui63 panicle, score: 98.135 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)
vg1127725153 C T -0.01 -0.01 -0.02 -0.02 -0.02 -0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1127725153 4.25E-06 2.61E-06 mr1440 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
vg1127725153 2.62E-06 NA mr1797 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
vg1127725153 2.62E-06 NA mr1801 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