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Detailed information for vg1125785739:

Variant ID: vg1125785739 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 25785739
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, T: 0.03, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:


TCCGGCCCATGGGTTGAATCTGCAGTGCAGGTGCTTTTGCAACCTGAACCCAAAGATAGCCTGAAGGAAATAGTTGGATATTCAGCCATGCACAATATTT[C/T]
AGACTTACAGTATTACAACAAACGAACAAAATTATTGTACTGCTCAAAACAAATTAATTGATAAAACTCATAACGTCAGCATCCATAATAATCTACTCCC

Reverse complement sequence

GGGAGTAGATTATTATGGATGCTGACGTTATGAGTTTTATCAATTAATTTGTTTTGAGCAGTACAATAATTTTGTTCGTTTGTTGTAATACTGTAAGTCT[G/A]
AAATATTGTGCATGGCTGAATATCCAACTATTTCCTTCAGGCTATCTTTGGGTTCAGGTTGCAAAAGCACCTGCACTGCAGATTCAACCCATGGGCCGGA

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 68.90% 18.40% 0.23% 12.40% NA
All Indica  2759 71.80% 9.20% 0.36% 18.63% NA
All Japonica  1512 59.90% 39.40% 0.00% 0.73% NA
Aus  269 83.60% 1.50% 0.00% 14.87% NA
Indica I  595 93.30% 2.40% 0.34% 4.03% NA
Indica II  465 44.10% 3.90% 0.43% 51.61% NA
Indica III  913 70.90% 17.50% 0.11% 11.50% NA
Indica Intermediate  786 73.20% 7.80% 0.64% 18.45% NA
Temperate Japonica  767 80.20% 18.80% 0.00% 1.04% NA
Tropical Japonica  504 31.70% 67.90% 0.00% 0.40% NA
Japonica Intermediate  241 53.90% 45.60% 0.00% 0.41% NA
VI/Aromatic  96 84.40% 0.00% 0.00% 15.62% NA
Intermediate  90 72.20% 20.00% 1.11% 6.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1125785739 C -> T LOC_Os11g42810.1 downstream_gene_variant ; 329.0bp to feature; MODIFIER silent_mutation Average:85.258; most accessible tissue: Callus, score: 97.401 N N N N
vg1125785739 C -> T LOC_Os11g42800-LOC_Os11g42810 intergenic_region ; MODIFIER silent_mutation Average:85.258; most accessible tissue: Callus, score: 97.401 N N N N
vg1125785739 C -> DEL N N silent_mutation Average:85.258; most accessible tissue: Callus, score: 97.401 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)
vg1125785739 C T -0.01 -0.09 -0.08 -0.06 -0.08 -0.08

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1125785739 NA 5.46E-08 mr1192 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
vg1125785739 NA 8.68E-08 mr1206 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
vg1125785739 NA 1.88E-07 mr1644 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
vg1125785739 NA 4.85E-13 mr1769 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
vg1125785739 1.46E-06 2.45E-09 mr1835 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
vg1125785739 NA 3.37E-06 mr1835 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
vg1125785739 NA 1.60E-09 mr1951 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
vg1125785739 NA 7.24E-06 mr1191_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
vg1125785739 NA 5.31E-07 mr1875_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
vg1125785739 NA 1.72E-06 mr1875_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
vg1125785739 NA 9.53E-06 mr1908_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
vg1125785739 NA 8.05E-07 mr1931_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