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Detailed information for vg0335647105:

Variant ID: vg0335647105 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 35647105
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:


TAAATAGACCCACAAGCAACAATAGTTCAAATATAAGAAAGGAAAAAAAAACATATTGCTTTATCTCGGAGGACATTTCGATCATAATTCCAACAATATT[C/T]
AGACGTGTGTATCCAACACACGTGTATGCGCGTTATGGTACTAACTGTGGACAACAACACTCTACACGAGACAATATGTAACATTAGGCGACAACAAAAA

Reverse complement sequence

TTTTTGTTGTCGCCTAATGTTACATATTGTCTCGTGTAGAGTGTTGTTGTCCACAGTTAGTACCATAACGCGCATACACGTGTGTTGGATACACACGTCT[G/A]
AATATTGTTGGAATTATGATCGAAATGTCCTCCGAGATAAAGCAATATGTTTTTTTTTCCTTTCTTATATTTGAACTATTGTTGCTTGTGGGTCTATTTA

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 76.80% 23.10% 0.04% 0.00% NA
All Indica  2759 89.20% 10.80% 0.07% 0.00% NA
All Japonica  1512 55.00% 45.00% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 98.00% 2.00% 0.00% 0.00% NA
Indica II  465 92.70% 7.30% 0.00% 0.00% NA
Indica III  913 83.10% 16.90% 0.00% 0.00% NA
Indica Intermediate  786 87.40% 12.30% 0.25% 0.00% NA
Temperate Japonica  767 90.40% 9.60% 0.00% 0.00% NA
Tropical Japonica  504 10.30% 89.70% 0.00% 0.00% NA
Japonica Intermediate  241 36.10% 63.90% 0.00% 0.00% NA
VI/Aromatic  96 11.50% 88.50% 0.00% 0.00% NA
Intermediate  90 66.70% 33.30% 0.00% 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
vg0335647105 C -> T LOC_Os03g63030.1 upstream_gene_variant ; 2756.0bp to feature; MODIFIER silent_mutation Average:72.097; most accessible tissue: Zhenshan97 flag leaf, score: 85.88 N N N N
vg0335647105 C -> T LOC_Os03g63040.1 upstream_gene_variant ; 564.0bp to feature; MODIFIER silent_mutation Average:72.097; most accessible tissue: Zhenshan97 flag leaf, score: 85.88 N N N N
vg0335647105 C -> T LOC_Os03g63030-LOC_Os03g63040 intergenic_region ; MODIFIER silent_mutation Average:72.097; most accessible tissue: Zhenshan97 flag leaf, score: 85.88 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)
vg0335647105 C T -0.01 0.0 0.0 -0.01 -0.01 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0335647105 NA 2.75E-06 mr1013 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
vg0335647105 NA 9.60E-06 mr1871 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
vg0335647105 NA 1.78E-08 mr1338_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
vg0335647105 NA 2.78E-06 mr1383_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
vg0335647105 NA 2.27E-11 mr1388_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
vg0335647105 NA 6.47E-09 mr1543_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
vg0335647105 NA 4.31E-12 mr1554_2 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
vg0335647105 NA 1.68E-06 mr1730_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
vg0335647105 NA 2.22E-10 mr1905_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
vg0335647105 NA 4.22E-08 mr1952_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
vg0335647105 NA 1.72E-08 mr1966_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
vg0335647105 NA 8.19E-07 mr1966_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