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Detailed information for vg0141603799:

Variant ID: vg0141603799 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 41603799
Reference Allele: CAlternative Allele: G
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.79, C: 0.21, others allele: 0.00, population size: 97. )

Flanking Sequence (100 bp) in Reference Genome:


GCATCGCCGTCATCGTCGACGTCGGCGACAAGGGCGCGGTGGCCAACCTCGCCAACAACCCCTCCGCCGCCGCCGACTGGGTCCGGAACAACGTCCAGGC[C/G]
TACTGGCCGAGCGTCTTCATCCGGTACATCGCCGTCGGCAACGAGCTCGGCCCCGGCGACATGGGGACCATCCTCCCGGCCATGCAGAACTTGTACAACG

Reverse complement sequence

CGTTGTACAAGTTCTGCATGGCCGGGAGGATGGTCCCCATGTCGCCGGGGCCGAGCTCGTTGCCGACGGCGATGTACCGGATGAAGACGCTCGGCCAGTA[G/C]
GCCTGGACGTTGTTCCGGACCCAGTCGGCGGCGGCGGAGGGGTTGTTGGCGAGGTTGGCCACCGCGCCCTTGTCGCCGACGTCGACGATGACGGCGATGC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 51.00% 48.60% 0.30% 0.13% NA
All Indica  2759 71.50% 27.80% 0.51% 0.18% NA
All Japonica  1512 2.40% 97.60% 0.00% 0.00% NA
Aus  269 97.80% 2.20% 0.00% 0.00% NA
Indica I  595 61.80% 37.00% 0.84% 0.34% NA
Indica II  465 77.60% 21.70% 0.43% 0.22% NA
Indica III  913 80.20% 19.20% 0.55% 0.11% NA
Indica Intermediate  786 65.30% 34.40% 0.25% 0.13% NA
Temperate Japonica  767 0.70% 99.30% 0.00% 0.00% NA
Tropical Japonica  504 3.60% 96.40% 0.00% 0.00% NA
Japonica Intermediate  241 5.40% 94.60% 0.00% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 46.70% 52.20% 0.00% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0141603799 C -> G LOC_Os01g71830.1 synonymous_variant ; p.Ala84Ala; LOW synonymous_codon Average:74.438; most accessible tissue: Zhenshan97 root, score: 93.988 N N N N
vg0141603799 C -> DEL LOC_Os01g71830.1 N frameshift_variant Average:74.438; most accessible tissue: Zhenshan97 root, score: 93.988 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)
vg0141603799 C G 0.0 0.0 -0.01 -0.01 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0141603799 NA 1.80E-07 mr1236 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
vg0141603799 NA 8.73E-06 mr1729 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
vg0141603799 1.68E-06 1.68E-06 mr1985 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
vg0141603799 NA 5.31E-06 mr1236_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
vg0141603799 NA 1.92E-12 mr1553_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
vg0141603799 NA 2.17E-07 mr1749_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
vg0141603799 NA 2.88E-08 mr1974_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
vg0141603799 NA 2.28E-07 mr1974_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