Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923).

Detailed information for vg0401152863:

Variant ID: vg0401152863 (JBrowse)Variation Type: INDEL
Chromosome: chr04Position: 1152863
Reference Allele: TAlternative Allele: A,TAA
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.69, A: 0.31, others allele: 0.00, population size: 58. )

Flanking Sequence (100 bp) in Reference Genome:


ATATTTGTATTAACACGTAATTAATTAAATATTAGATTTTTTCCCCCCTAAAATGGATCATTATGATTTTTTAAGCAACTTTCGTATATAGATTTTTTTT[T/A,TAA]
AAAAAACACACCGTTTAATAGTTTGAAAAGCATGCGCGCGGAAAACAAGGGTGAGGAGTTGAGAACTCCCAGCAAAGAACTGGCCTAAGTTTCTTTCAAC

Reverse complement sequence

GTTGAAAGAAACTTAGGCCAGTTCTTTGCTGGGAGTTCTCAACTCCTCACCCTTGTTTTCCGCGCGCATGCTTTTCAAACTATTAAACGGTGTGTTTTTT[A/T,TTA]
AAAAAAAATCTATATACGAAAGTTGCTTAAAAAATCATAATGATCCATTTTAGGGGGGAAAAAATCTAATATTTAATTAATTACGTGTTAATACAAATAT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 75.50% 23.30% 1.10% 0.00% TAA: 0.02%
All Indica  2759 87.20% 12.10% 0.76% 0.00% NA
All Japonica  1512 49.90% 48.30% 1.72% 0.00% NA
Aus  269 96.30% 3.70% 0.00% 0.00% NA
Indica I  595 99.00% 1.00% 0.00% 0.00% NA
Indica II  465 75.30% 21.70% 3.01% 0.00% NA
Indica III  913 81.50% 18.20% 0.33% 0.00% NA
Indica Intermediate  786 91.90% 7.60% 0.51% 0.00% NA
Temperate Japonica  767 22.40% 76.80% 0.78% 0.00% NA
Tropical Japonica  504 77.40% 19.00% 3.57% 0.00% NA
Japonica Intermediate  241 80.10% 19.10% 0.83% 0.00% NA
VI/Aromatic  96 91.70% 7.30% 1.04% 0.00% NA
Intermediate  90 70.00% 24.40% 4.44% 0.00% TAA: 1.11%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0401152863 T -> TAA LOC_Os04g02910.1 upstream_gene_variant ; 645.0bp to feature; MODIFIER silent_mutation Average:84.088; most accessible tissue: Zhenshan97 flag leaf, score: 93.175 N N N N
vg0401152863 T -> TAA LOC_Os04g02910.3 upstream_gene_variant ; 1437.0bp to feature; MODIFIER silent_mutation Average:84.088; most accessible tissue: Zhenshan97 flag leaf, score: 93.175 N N N N
vg0401152863 T -> TAA LOC_Os04g02910.4 upstream_gene_variant ; 645.0bp to feature; MODIFIER silent_mutation Average:84.088; most accessible tissue: Zhenshan97 flag leaf, score: 93.175 N N N N
vg0401152863 T -> TAA LOC_Os04g02910-LOC_Os04g02920 intergenic_region ; MODIFIER silent_mutation Average:84.088; most accessible tissue: Zhenshan97 flag leaf, score: 93.175 N N N N
vg0401152863 T -> A LOC_Os04g02910.1 upstream_gene_variant ; 644.0bp to feature; MODIFIER silent_mutation Average:84.088; most accessible tissue: Zhenshan97 flag leaf, score: 93.175 N N N N
vg0401152863 T -> A LOC_Os04g02910.3 upstream_gene_variant ; 1436.0bp to feature; MODIFIER silent_mutation Average:84.088; most accessible tissue: Zhenshan97 flag leaf, score: 93.175 N N N N
vg0401152863 T -> A LOC_Os04g02910.4 upstream_gene_variant ; 644.0bp to feature; MODIFIER silent_mutation Average:84.088; most accessible tissue: Zhenshan97 flag leaf, score: 93.175 N N N N
vg0401152863 T -> A LOC_Os04g02910-LOC_Os04g02920 intergenic_region ; MODIFIER silent_mutation Average:84.088; most accessible tissue: Zhenshan97 flag leaf, score: 93.175 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)
vg0401152863 T A 0.0 0.0 0.0 0.0 0.0 0.0
vg0401152863 T TAA -0.09 -0.13 -0.02 0.11 -0.03 -0.1

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0401152863 NA 8.55E-10 Heading_date 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
vg0401152863 NA 2.70E-06 mr1002 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
vg0401152863 4.98E-06 NA mr1174 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
vg0401152863 NA 2.54E-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
vg0401152863 NA 3.26E-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
vg0401152863 NA 1.94E-06 mr1205 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
vg0401152863 NA 2.75E-08 mr1229 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
vg0401152863 NA 5.10E-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
vg0401152863 NA 2.07E-08 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
vg0401152863 NA 1.33E-06 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
vg0401152863 NA 5.96E-07 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
vg0401152863 NA 9.71E-06 mr1550 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
vg0401152863 NA 4.80E-06 mr1596 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
vg0401152863 NA 7.75E-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
vg0401152863 NA 2.22E-06 mr1668 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
vg0401152863 NA 6.16E-07 mr1729 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
vg0401152863 NA 2.25E-06 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
vg0401152863 NA 2.98E-10 mr1880 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
vg0401152863 NA 4.70E-06 mr1882 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
vg0401152863 NA 1.13E-06 mr1229_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
vg0401152863 NA 2.50E-08 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
vg0401152863 NA 5.81E-06 mr1252_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
vg0401152863 NA 9.63E-06 mr1544_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
vg0401152863 NA 5.66E-06 mr1627_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
vg0401152863 NA 3.38E-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
vg0401152863 NA 1.62E-07 mr1748_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
vg0401152863 NA 3.73E-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
vg0401152863 NA 1.22E-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
vg0401152863 NA 8.48E-06 mr1902_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
vg0401152863 NA 2.09E-08 mr1952_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