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Detailed information for vg0425010504:

Variant ID: vg0425010504 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 25010504
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CACTCTTCTCTCGCAGTCGCATGCCGGCCGACGGGTAGGGAGCAGACGCCCGGGCGGCGGCCGGCGGACCGCAGCGTGCGAAGGCGTCCTCGCCCTCGTC[T/C]
TCGTATGCCGAGGACGAGCGCCGCGTTGAGGCCTTCCACCAGCGGTTCGGCACCGGCGCGACGGAGATGCCAACTTGCTTGGCACCGCTCGCCGCCGCCC

Reverse complement sequence

GGGCGGCGGCGAGCGGTGCCAAGCAAGTTGGCATCTCCGTCGCGCCGGTGCCGAACCGCTGGTGGAAGGCCTCAACGCGGCGCTCGTCCTCGGCATACGA[A/G]
GACGAGGGCGAGGACGCCTTCGCACGCTGCGGTCCGCCGGCCGCCGCCCGGGCGTCTGCTCCCTACCCGTCGGCCGGCATGCGACTGCGAGAGAAGAGTG

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 83.30% 16.10% 0.57% 0.00% NA
All Indica  2759 98.30% 1.50% 0.14% 0.00% NA
All Japonica  1512 53.00% 45.70% 1.26% 0.00% NA
Aus  269 97.80% 0.70% 1.49% 0.00% NA
Indica I  595 96.80% 2.90% 0.34% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.70% 0.30% 0.00% 0.00% NA
Indica Intermediate  786 97.10% 2.70% 0.25% 0.00% NA
Temperate Japonica  767 14.10% 84.10% 1.83% 0.00% NA
Tropical Japonica  504 97.40% 2.00% 0.60% 0.00% NA
Japonica Intermediate  241 84.20% 14.90% 0.83% 0.00% NA
VI/Aromatic  96 87.50% 12.50% 0.00% 0.00% NA
Intermediate  90 84.40% 15.60% 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
vg0425010504 T -> C LOC_Os04g42270.1 upstream_gene_variant ; 509.0bp to feature; MODIFIER silent_mutation Average:97.423; most accessible tissue: Zhenshan97 panicle, score: 98.349 N N N N
vg0425010504 T -> C LOC_Os04g42280.1 upstream_gene_variant ; 1477.0bp to feature; MODIFIER silent_mutation Average:97.423; most accessible tissue: Zhenshan97 panicle, score: 98.349 N N N N
vg0425010504 T -> C LOC_Os04g42270.2 upstream_gene_variant ; 477.0bp to feature; MODIFIER silent_mutation Average:97.423; most accessible tissue: Zhenshan97 panicle, score: 98.349 N N N N
vg0425010504 T -> C LOC_Os04g42260.1 downstream_gene_variant ; 3883.0bp to feature; MODIFIER silent_mutation Average:97.423; most accessible tissue: Zhenshan97 panicle, score: 98.349 N N N N
vg0425010504 T -> C LOC_Os04g42270-LOC_Os04g42280 intergenic_region ; MODIFIER silent_mutation Average:97.423; most accessible tissue: Zhenshan97 panicle, score: 98.349 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)
vg0425010504 T C 0.01 0.01 0.02 0.02 0.02 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0425010504 NA 4.71E-08 mr1077 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
vg0425010504 NA 5.33E-12 mr1182 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
vg0425010504 NA 2.25E-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
vg0425010504 NA 1.64E-07 mr1202 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
vg0425010504 NA 1.70E-07 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
vg0425010504 NA 1.72E-07 mr1252 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
vg0425010504 NA 1.98E-07 mr1330 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
vg0425010504 NA 3.95E-06 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
vg0425010504 NA 2.79E-06 mr1521 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
vg0425010504 NA 1.92E-07 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
vg0425010504 NA 1.24E-06 mr1629 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
vg0425010504 NA 3.64E-06 mr1763 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
vg0425010504 3.70E-06 3.70E-06 mr1802 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
vg0425010504 NA 9.73E-09 mr1844 Jap_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
vg0425010504 NA 8.15E-08 mr1880 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
vg0425010504 NA 2.04E-13 mr1880 Jap_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
vg0425010504 NA 2.33E-06 mr1977 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
vg0425010504 NA 4.15E-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
vg0425010504 NA 1.76E-06 mr1077_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
vg0425010504 NA 3.46E-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
vg0425010504 NA 7.04E-07 mr1952_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