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Detailed information for vg0204869094:

Variant ID: vg0204869094 (JBrowse)Variation Type: INDEL
Chromosome: chr02Position: 4869094
Reference Allele: CAlternative Allele: T,CATTTCAGAGCATT
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, C: 0.00, others allele: 0.00, population size: 300. )

Flanking Sequence (100 bp) in Reference Genome:


GTCGAAGACTACTTGGGCATCGATCAGATGTGCGAGTTGAAAGTGATAGTAGTAGCAGCATGCTGTACTAGCAGTACGCATATTGGACATTTCAGAGCAT[C/T,CATTTCAGAGCATT]
TAACTTTTAAATGTGGCAATTAAGGATTTACCAACCACAATCTATAACATATGGGTAATCTTTAATTGCCACTTTAAATAGTTAAATATTTTTATTTTGG

Reverse complement sequence

CCAAAATAAAAATATTTAACTATTTAAAGTGGCAATTAAAGATTACCCATATGTTATAGATTGTGGTTGGTAAATCCTTAATTGCCACATTTAAAAGTTA[G/A,AATGCTCTGAAATG]
ATGCTCTGAAATGTCCAATATGCGTACTGCTAGTACAGCATGCTGCTACTACTATCACTTTCAACTCGCACATCTGATCGATGCCCAAGTAGTCTTCGAC

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 73.50% 26.40% 0.06% 0.00% CATTTCAGAGCATT: 0.02%
All Indica  2759 91.80% 8.20% 0.00% 0.00% NA
All Japonica  1512 34.00% 65.80% 0.20% 0.00% NA
Aus  269 99.60% 0.00% 0.00% 0.00% CATTTCAGAGCATT: 0.37%
Indica I  595 99.20% 0.80% 0.00% 0.00% NA
Indica II  465 87.10% 12.90% 0.00% 0.00% NA
Indica III  913 89.00% 11.00% 0.00% 0.00% NA
Indica Intermediate  786 92.40% 7.60% 0.00% 0.00% NA
Temperate Japonica  767 6.30% 93.70% 0.00% 0.00% NA
Tropical Japonica  504 65.90% 33.90% 0.20% 0.00% NA
Japonica Intermediate  241 55.60% 43.60% 0.83% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 70.00% 30.00% 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
vg0204869094 C -> T LOC_Os02g09480.1 3_prime_UTR_variant ; 449.0bp to feature; MODIFIER silent_mutation Average:95.689; most accessible tissue: Minghui63 young leaf, score: 98.441 N N N N
vg0204869094 C -> T LOC_Os02g09490.1 downstream_gene_variant ; 1048.0bp to feature; MODIFIER silent_mutation Average:95.689; most accessible tissue: Minghui63 young leaf, score: 98.441 N N N N
vg0204869094 C -> CATTTCAGAGCATT LOC_Os02g09480.1 3_prime_UTR_variant ; 450.0bp to feature; MODIFIER silent_mutation Average:95.689; most accessible tissue: Minghui63 young leaf, score: 98.441 N N N N
vg0204869094 C -> CATTTCAGAGCATT LOC_Os02g09490.1 downstream_gene_variant ; 1047.0bp to feature; MODIFIER silent_mutation Average:95.689; most accessible tissue: Minghui63 young leaf, score: 98.441 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)
vg0204869094 C CATTT* 0.06 0.18 -0.02 0.15 0.08 0.15
vg0204869094 C T 0.01 0.01 -0.02 0.0 -0.02 -0.05

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0204869094 NA 8.33E-12 mr1069 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
vg0204869094 NA 1.25E-13 mr1149 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
vg0204869094 NA 2.19E-07 mr1206 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
vg0204869094 NA 1.84E-09 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
vg0204869094 NA 3.67E-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
vg0204869094 NA 6.23E-06 mr1246_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
vg0204869094 NA 7.43E-07 mr1404_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
vg0204869094 NA 3.11E-07 mr1555_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
vg0204869094 NA 3.41E-06 mr1620_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
vg0204869094 NA 2.44E-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
vg0204869094 NA 6.37E-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