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Detailed information for vg0431612471:

Variant ID: vg0431612471 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 31612471
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.89, T: 0.11, others allele: 0.00, population size: 84. )

Flanking Sequence (100 bp) in Reference Genome:


AGCAGTTGTAGCTCTATTAAAAATGCGAATATTAAGGAATGATCTAATATCAAATAATTAGAAGGGGTGAGGTTTCGAACCCAGATCATCTAGCCCACCA[T/C]
CTTATAGAGCTAGTTGGAAGACCCCTGAATGTGTTTCTGTTGTAGCTCTATTAAACAAGCCCTTAGCAGCATCTTGTGATTCATCCGTGTGTTTCTCCGG

Reverse complement sequence

CCGGAGAAACACACGGATGAATCACAAGATGCTGCTAAGGGCTTGTTTAATAGAGCTACAACAGAAACACATTCAGGGGTCTTCCAACTAGCTCTATAAG[A/G]
TGGTGGGCTAGATGATCTGGGTTCGAAACCTCACCCCTTCTAATTATTTGATATTAGATCATTCCTTAATATTCGCATTTTTAATAGAGCTACAACTGCT

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 61.00% 23.60% 0.85% 14.52% NA
All Indica  2759 82.10% 7.80% 0.72% 9.39% NA
All Japonica  1512 24.30% 55.50% 1.06% 19.18% NA
Aus  269 51.70% 13.40% 0.74% 34.20% NA
Indica I  595 79.80% 16.50% 1.01% 2.69% NA
Indica II  465 86.50% 5.80% 0.43% 7.31% NA
Indica III  913 81.60% 4.20% 0.22% 14.02% NA
Indica Intermediate  786 81.90% 6.50% 1.27% 10.31% NA
Temperate Japonica  767 8.20% 84.50% 1.30% 6.00% NA
Tropical Japonica  504 40.30% 24.60% 0.60% 34.52% NA
Japonica Intermediate  241 41.90% 27.80% 1.24% 29.05% NA
VI/Aromatic  96 68.80% 2.10% 1.04% 28.12% NA
Intermediate  90 51.10% 27.80% 1.11% 20.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0431612471 T -> C LOC_Os04g53070.1 upstream_gene_variant ; 1637.0bp to feature; MODIFIER silent_mutation Average:85.923; most accessible tissue: Minghui63 flower, score: 96.697 N N N N
vg0431612471 T -> C LOC_Os04g53080.1 upstream_gene_variant ; 864.0bp to feature; MODIFIER silent_mutation Average:85.923; most accessible tissue: Minghui63 flower, score: 96.697 N N N N
vg0431612471 T -> C LOC_Os04g53060.1 downstream_gene_variant ; 2602.0bp to feature; MODIFIER silent_mutation Average:85.923; most accessible tissue: Minghui63 flower, score: 96.697 N N N N
vg0431612471 T -> C LOC_Os04g53070-LOC_Os04g53080 intergenic_region ; MODIFIER silent_mutation Average:85.923; most accessible tissue: Minghui63 flower, score: 96.697 N N N N
vg0431612471 T -> DEL N N silent_mutation Average:85.923; most accessible tissue: Minghui63 flower, score: 96.697 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)
vg0431612471 T C -0.04 0.0 0.0 -0.02 -0.03 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0431612471 NA 1.19E-15 Plant_height Jap_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0431612471 NA 3.58E-12 Spikelet_length Jap_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0431612471 NA 2.01E-07 mr1044 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
vg0431612471 NA 1.14E-06 mr1082 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
vg0431612471 NA 1.51E-07 mr1164 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
vg0431612471 NA 5.60E-06 mr1169 Ind_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
vg0431612471 NA 9.60E-06 mr1180 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
vg0431612471 NA 1.50E-06 mr1183 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
vg0431612471 NA 1.26E-06 mr1252 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
vg0431612471 NA 7.34E-06 mr1482 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
vg0431612471 NA 6.58E-07 mr1503 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
vg0431612471 NA 3.86E-07 mr1617 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
vg0431612471 NA 9.07E-08 mr1627 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
vg0431612471 NA 1.50E-07 mr1723 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
vg0431612471 NA 7.85E-07 mr1748 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
vg0431612471 NA 1.23E-07 mr1010_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
vg0431612471 NA 3.27E-10 mr1011_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
vg0431612471 NA 5.56E-06 mr1063_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
vg0431612471 NA 5.37E-08 mr1137_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
vg0431612471 NA 6.48E-07 mr1161_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
vg0431612471 NA 3.73E-09 mr1164_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
vg0431612471 NA 1.03E-07 mr1183_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
vg0431612471 NA 1.37E-06 mr1194_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
vg0431612471 NA 1.26E-07 mr1229_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
vg0431612471 NA 1.57E-07 mr1252_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
vg0431612471 NA 1.60E-09 mr1482_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
vg0431612471 NA 3.48E-09 mr1486_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
vg0431612471 NA 8.50E-11 mr1521_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
vg0431612471 NA 5.47E-07 mr1570_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
vg0431612471 NA 5.88E-12 mr1580_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
vg0431612471 NA 2.66E-06 mr1617_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
vg0431612471 NA 4.11E-06 mr1668_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
vg0431612471 NA 7.18E-06 mr1723_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
vg0431612471 NA 1.90E-11 mr1825_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
vg0431612471 NA 3.34E-07 mr1880_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
vg0431612471 NA 1.76E-08 mr1880_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