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Detailed information for vg1107621144:

Variant ID: vg1107621144 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 7621144
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 123. )

Flanking Sequence (100 bp) in Reference Genome:


GCCTCCTGTCCAATGGCCCAATATGCGGCCCATGGCTGGCTTATACTAGGCTCTCTTCCAGCCGACCACAGTAAACACTAAGGGCCTGTTCACTTTGATG[C/T]
CATTTCCAACCTTACCAAATTTTGGTAAAGTTGCCAAAAAAGTGGCTATATTTAGTTTGCTGCCAAATTTTGAGAACTATATAAGAAATCCTACCAAAAT

Reverse complement sequence

ATTTTGGTAGGATTTCTTATATAGTTCTCAAAATTTGGCAGCAAACTAAATATAGCCACTTTTTTGGCAACTTTACCAAAATTTGGTAAGGTTGGAAATG[G/A]
CATCAAAGTGAACAGGCCCTTAGTGTTTACTGTGGTCGGCTGGAAGAGAGCCTAGTATAAGCCAGCCATGGGCCGCATATTGGGCCATTGGACAGGAGGC

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 75.80% 23.30% 0.91% 0.00% NA
All Indica  2759 72.20% 27.60% 0.14% 0.00% NA
All Japonica  1512 76.40% 21.20% 2.38% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 92.40% 7.60% 0.00% 0.00% NA
Indica II  465 40.60% 59.10% 0.22% 0.00% NA
Indica III  913 75.40% 24.60% 0.00% 0.00% NA
Indica Intermediate  786 72.00% 27.60% 0.38% 0.00% NA
Temperate Japonica  767 96.20% 1.00% 2.74% 0.00% NA
Tropical Japonica  504 40.70% 57.50% 1.79% 0.00% NA
Japonica Intermediate  241 88.00% 9.50% 2.49% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 78.90% 17.80% 3.33% 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
vg1107621144 C -> T LOC_Os11g13820.1 downstream_gene_variant ; 2409.0bp to feature; MODIFIER silent_mutation Average:95.109; most accessible tissue: Minghui63 root, score: 99.109 N N N N
vg1107621144 C -> T LOC_Os11g13830.1 downstream_gene_variant ; 900.0bp to feature; MODIFIER silent_mutation Average:95.109; most accessible tissue: Minghui63 root, score: 99.109 N N N N
vg1107621144 C -> T LOC_Os11g13830-LOC_Os11g13840 intergenic_region ; MODIFIER silent_mutation Average:95.109; most accessible tissue: Minghui63 root, score: 99.109 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)
vg1107621144 C T 0.0 0.0 0.01 0.0 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1107621144 NA 9.66E-14 Grain_length 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
vg1107621144 NA 1.01E-06 mr1047 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
vg1107621144 NA 3.05E-06 mr1422 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
vg1107621144 NA 2.10E-06 mr1471 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
vg1107621144 NA 4.52E-07 mr1479 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
vg1107621144 NA 9.68E-08 mr1502 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
vg1107621144 NA 2.73E-06 mr1502 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
vg1107621144 NA 1.86E-08 mr1543 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
vg1107621144 NA 8.40E-07 mr1642 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
vg1107621144 NA 4.40E-07 mr1742 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
vg1107621144 5.58E-07 1.53E-11 mr1742 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
vg1107621144 NA 1.19E-11 mr1794 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
vg1107621144 NA 2.30E-06 mr1892 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
vg1107621144 NA 2.32E-06 mr1975 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
vg1107621144 NA 1.47E-06 mr1990 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
vg1107621144 NA 4.05E-07 mr1047_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
vg1107621144 NA 2.28E-07 mr1149_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
vg1107621144 NA 3.62E-12 mr1794_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
vg1107621144 NA 3.32E-06 mr1850_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
vg1107621144 NA 8.97E-06 mr1959_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