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Detailed information for vg1125768032:

Variant ID: vg1125768032 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 25768032
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.68, T: 0.32, others allele: 0.00, population size: 59. )

Flanking Sequence (100 bp) in Reference Genome:


ACACACGGCCCAGGCACGGCCCAACACGACACGGGCCGTGCCGGGCCGGCCCGAAGGCACGACGGCCCATCGTGCTTTTTCACAGATTAAGTCTAATTTT[C/T]
CTCCCTCCTCTTGGGCTGTGGCATATACATAGCTAAAAAGTCTATTTTTTCTCCCTCTTCTTTGTTCTGTGACATATAAATAGTTAAAAATAAATCTATT

Reverse complement sequence

AATAGATTTATTTTTAACTATTTATATGTCACAGAACAAAGAAGAGGGAGAAAAAATAGACTTTTTAGCTATGTATATGCCACAGCCCAAGAGGAGGGAG[G/A]
AAAATTAGACTTAATCTGTGAAAAAGCACGATGGGCCGTCGTGCCTTCGGGCCGGCCCGGCACGGCCCGTGTCGTGTTGGGCCGTGCCTGGGCCGTGTGT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 22.10% 21.20% 4.82% 51.93% NA
All Indica  2759 19.10% 18.80% 4.28% 57.88% NA
All Japonica  1512 22.40% 30.10% 3.77% 43.78% NA
Aus  269 41.30% 2.60% 4.46% 51.67% NA
Indica I  595 40.30% 36.80% 0.84% 22.02% NA
Indica II  465 8.60% 21.90% 6.02% 63.44% NA
Indica III  913 15.70% 11.10% 4.49% 68.78% NA
Indica Intermediate  786 13.10% 12.20% 5.60% 69.08% NA
Temperate Japonica  767 24.30% 49.50% 3.13% 23.08% NA
Tropical Japonica  504 13.90% 9.30% 4.56% 72.22% NA
Japonica Intermediate  241 34.00% 11.60% 4.15% 50.21% NA
VI/Aromatic  96 50.00% 1.00% 37.50% 11.46% NA
Intermediate  90 22.20% 22.20% 5.56% 50.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1125768032 C -> T LOC_Os11g42770.1 downstream_gene_variant ; 4817.0bp to feature; MODIFIER silent_mutation Average:92.514; most accessible tissue: Zhenshan97 panicle, score: 99.987 N N N N
vg1125768032 C -> T LOC_Os11g42780.1 downstream_gene_variant ; 937.0bp to feature; MODIFIER silent_mutation Average:92.514; most accessible tissue: Zhenshan97 panicle, score: 99.987 N N N N
vg1125768032 C -> T LOC_Os11g42790.1 downstream_gene_variant ; 433.0bp to feature; MODIFIER silent_mutation Average:92.514; most accessible tissue: Zhenshan97 panicle, score: 99.987 N N N N
vg1125768032 C -> T LOC_Os11g42780-LOC_Os11g42790 intergenic_region ; MODIFIER silent_mutation Average:92.514; most accessible tissue: Zhenshan97 panicle, score: 99.987 N N N N
vg1125768032 C -> DEL N N silent_mutation Average:92.514; most accessible tissue: Zhenshan97 panicle, score: 99.987 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)
vg1125768032 C T -0.03 -0.04 -0.04 -0.04 -0.04 -0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1125768032 2.39E-12 5.42E-20 mr1191 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
vg1125768032 1.02E-16 6.56E-20 mr1191 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
vg1125768032 NA 2.18E-07 mr1530 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
vg1125768032 1.44E-12 4.82E-22 mr1644 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
vg1125768032 2.05E-19 9.91E-23 mr1644 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
vg1125768032 NA 1.22E-07 mr1662 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
vg1125768032 2.41E-06 1.74E-10 mr1662 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
vg1125768032 NA 5.02E-08 mr1745 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
vg1125768032 9.30E-06 9.30E-06 mr1046_2 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
vg1125768032 1.43E-16 1.15E-34 mr1191_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
vg1125768032 4.57E-27 1.06E-34 mr1191_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
vg1125768032 2.11E-06 2.11E-06 mr1290_2 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
vg1125768032 8.43E-07 3.39E-06 mr1298_2 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
vg1125768032 3.79E-06 3.79E-06 mr1366_2 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
vg1125768032 NA 1.88E-07 mr1380_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
vg1125768032 NA 6.90E-08 mr1530_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
vg1125768032 3.34E-07 1.38E-06 mr1545_2 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
vg1125768032 NA 4.90E-07 mr1561_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
vg1125768032 2.53E-07 3.30E-07 mr1566_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
vg1125768032 5.77E-06 5.77E-06 mr1643_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
vg1125768032 3.50E-06 3.50E-06 mr1661_2 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
vg1125768032 NA 1.42E-06 mr1662_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
vg1125768032 NA 3.53E-11 mr1662_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
vg1125768032 1.28E-06 NA mr1739_2 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
vg1125768032 NA 2.84E-11 mr1745_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
vg1125768032 4.03E-06 4.03E-06 mr1752_2 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
vg1125768032 7.85E-06 NA mr1873_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
vg1125768032 5.32E-07 2.75E-06 mr1874_2 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
vg1125768032 NA 2.62E-07 mr1875_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
vg1125768032 NA 1.36E-07 mr1908_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
vg1125768032 3.69E-06 3.69E-06 mr1953_2 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
vg1125768032 3.99E-06 3.99E-06 mr1967_2 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
vg1125768032 2.14E-06 2.14E-06 mr1987_2 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