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Detailed information for vg0142727279:

Variant ID: vg0142727279 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 42727279
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.88, C: 0.11, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:


TATGTAGAATAGATGTGCACGGGCGCACGTGTTTCATCCCTCTAATTCTGAATCCCCACGTGACGATCGAGCTTAAAGCCGAACGGGCGGGGCGGGGGGA[T/C]
AAAGCGGGTCCCCCAGCCGCTGTCTCCAGTTCACACCCACAACCCGAAGTCGATCGCTCGTGTTCGTGTCCGCCTCGACGGCGAACTCGACGGGTCCCGA

Reverse complement sequence

TCGGGACCCGTCGAGTTCGCCGTCGAGGCGGACACGAACACGAGCGATCGACTTCGGGTTGTGGGTGTGAACTGGAGACAGCGGCTGGGGGACCCGCTTT[A/G]
TCCCCCCGCCCCGCCCGTTCGGCTTTAAGCTCGATCGTCACGTGGGGATTCAGAATTAGAGGGATGAAACACGTGCGCCCGTGCACATCTATTCTACATA

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 53.50% 46.20% 0.28% 0.00% NA
All Indica  2759 68.80% 30.80% 0.36% 0.00% NA
All Japonica  1512 17.30% 82.50% 0.13% 0.00% NA
Aus  269 91.40% 8.60% 0.00% 0.00% NA
Indica I  595 64.20% 35.50% 0.34% 0.00% NA
Indica II  465 72.90% 26.70% 0.43% 0.00% NA
Indica III  913 75.80% 24.00% 0.22% 0.00% NA
Indica Intermediate  786 61.80% 37.70% 0.51% 0.00% NA
Temperate Japonica  767 5.90% 94.10% 0.00% 0.00% NA
Tropical Japonica  504 25.00% 74.60% 0.40% 0.00% NA
Japonica Intermediate  241 37.80% 62.20% 0.00% 0.00% NA
VI/Aromatic  96 79.20% 20.80% 0.00% 0.00% NA
Intermediate  90 51.10% 47.80% 1.11% 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
vg0142727279 T -> C LOC_Os01g73770.1 upstream_gene_variant ; 147.0bp to feature; MODIFIER silent_mutation Average:99.12; most accessible tissue: Callus, score: 99.874 N N N N
vg0142727279 T -> C LOC_Os01g73760.1 downstream_gene_variant ; 512.0bp to feature; MODIFIER silent_mutation Average:99.12; most accessible tissue: Callus, score: 99.874 N N N N
vg0142727279 T -> C LOC_Os01g73760-LOC_Os01g73770 intergenic_region ; MODIFIER silent_mutation Average:99.12; most accessible tissue: Callus, score: 99.874 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)
vg0142727279 T C -0.06 -0.14 -0.12 -0.09 -0.06 -0.05

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0142727279 NA 4.44E-07 mr1038 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
vg0142727279 NA 3.58E-12 mr1170 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
vg0142727279 NA 5.89E-07 mr1170 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
vg0142727279 NA 4.49E-07 mr1177 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
vg0142727279 NA 6.03E-06 mr1236 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
vg0142727279 NA 3.35E-08 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
vg0142727279 NA 3.45E-09 mr1389 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
vg0142727279 NA 5.29E-07 mr1807 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
vg0142727279 NA 3.57E-07 mr1909 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
vg0142727279 NA 1.15E-06 mr1974 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
vg0142727279 NA 5.31E-09 mr1974 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
vg0142727279 7.63E-06 7.63E-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
vg0142727279 NA 3.55E-08 mr1038_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
vg0142727279 NA 6.86E-10 mr1170_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
vg0142727279 NA 9.94E-08 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
vg0142727279 NA 3.64E-07 mr1517_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
vg0142727279 NA 2.13E-08 mr1855_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
vg0142727279 NA 8.47E-06 mr1968_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
vg0142727279 3.18E-08 8.77E-13 mr1974_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
vg0142727279 5.95E-07 2.14E-09 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