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Detailed information for vg0404301610:

Variant ID: vg0404301610 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 4301610
Reference Allele: CAlternative Allele: T,A
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, T: 0.00, others allele: 0.00, population size: 186. )

Flanking Sequence (100 bp) in Reference Genome:


TGAGCTAGCTTAATTAGACCATCCATATACATGAGATCAGTTTTTAGCATATTCTTTTCATTGACAAGCTAGTTTTTCTCAGTATTATTCATATATAATA[C/T,A]
TATACTCAGCTGACCTAATATGTATTTCTATACCTGCACAATTCGATCTTATCTCTCAACTCTCTCTCCATTTTTTTTCTACACACAAAAAAGCAATTCT

Reverse complement sequence

AGAATTGCTTTTTTGTGTGTAGAAAAAAAATGGAGAGAGAGTTGAGAGATAAGATCGAATTGTGCAGGTATAGAAATACATATTAGGTCAGCTGAGTATA[G/A,T]
TATTATATATGAATAATACTGAGAAAAACTAGCTTGTCAATGAAAAGAATATGCTAAAAACTGATCTCATGTATATGGATGGTCTAATTAAGCTAGCTCA

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 66.80% 30.30% 0.08% 0.00% A: 2.77%
All Indica  2759 66.50% 31.20% 0.04% 0.00% A: 2.25%
All Japonica  1512 69.00% 30.60% 0.13% 0.00% A: 0.33%
Aus  269 65.10% 14.50% 0.00% 0.00% A: 20.45%
Indica I  595 95.60% 4.40% 0.00% 0.00% NA
Indica II  465 78.70% 17.20% 0.00% 0.00% A: 4.09%
Indica III  913 39.90% 57.60% 0.11% 0.00% A: 2.41%
Indica Intermediate  786 68.30% 29.00% 0.00% 0.00% A: 2.67%
Temperate Japonica  767 94.30% 5.70% 0.00% 0.00% NA
Tropical Japonica  504 28.00% 71.40% 0.40% 0.00% A: 0.20%
Japonica Intermediate  241 74.30% 24.10% 0.00% 0.00% A: 1.66%
VI/Aromatic  96 52.10% 44.80% 1.04% 0.00% A: 2.08%
Intermediate  90 61.10% 31.10% 0.00% 0.00% A: 7.78%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0404301610 C -> A LOC_Os04g08060.1 downstream_gene_variant ; 4039.0bp to feature; MODIFIER silent_mutation Average:72.067; most accessible tissue: Zhenshan97 root, score: 96.006 N N N N
vg0404301610 C -> A LOC_Os04g08060-LOC_Os04g08070 intergenic_region ; MODIFIER silent_mutation Average:72.067; most accessible tissue: Zhenshan97 root, score: 96.006 N N N N
vg0404301610 C -> T LOC_Os04g08060.1 downstream_gene_variant ; 4039.0bp to feature; MODIFIER silent_mutation Average:72.067; most accessible tissue: Zhenshan97 root, score: 96.006 N N N N
vg0404301610 C -> T LOC_Os04g08060-LOC_Os04g08070 intergenic_region ; MODIFIER silent_mutation Average:72.067; most accessible tissue: Zhenshan97 root, score: 96.006 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)
vg0404301610 C A 0.0 0.0 -0.02 -0.02 -0.03 -0.01
vg0404301610 C T 0.05 0.0 -0.03 -0.01 -0.04 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0404301610 NA 1.11E-06 mr1037 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
vg0404301610 NA 4.15E-14 mr1301 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
vg0404301610 NA 3.85E-07 mr1993 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
vg0404301610 NA 4.05E-08 mr1993 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
vg0404301610 NA 1.42E-07 mr1037_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
vg0404301610 NA 1.87E-07 mr1121_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
vg0404301610 4.63E-06 4.63E-06 mr1574_2 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
vg0404301610 NA 6.95E-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
vg0404301610 NA 2.49E-10 mr1771_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
vg0404301610 NA 1.97E-10 mr1784_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
vg0404301610 NA 1.56E-07 mr1798_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
vg0404301610 NA 1.04E-08 mr1800_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