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Detailed information for vg0222065930:

Variant ID: vg0222065930 (JBrowse)Variation Type: INDEL
Chromosome: chr02Position: 22065930
Reference Allele: TAlternative Allele: A,TA
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.93, A: 0.06, others allele: 0.00, population size: 177. )

Flanking Sequence (100 bp) in Reference Genome:


GTCTTTGACGGCGATGGCTATGGCCGTGAAAACGGTCACGGAAATTTTCGATAGATAGAACATCGCTTTTGCGAAAGTAGCATGGGCTGTAAATTTTTTT[T/A,TA]
AAAAAAAAACTTTTATGCCGTACTGTAATTATCATTCAAGAGTTAAACTGTAACTTTCTAATTAATCGTTTATAAGTAGAACGACCTTTTCACCACTGCG

Reverse complement sequence

CGCAGTGGTGAAAAGGTCGTTCTACTTATAAACGATTAATTAGAAAGTTACAGTTTAACTCTTGAATGATAATTACAGTACGGCATAAAAGTTTTTTTTT[A/T,TA]
AAAAAAATTTACAGCCCATGCTACTTTCGCAAAAGCGATGTTCTATCTATCGAAAATTTCCGTGACCGTTTTCACGGCCATAGCCATCGCCGTCAAAGAC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 59.70% 36.80% 3.13% 0.00% TA: 0.38%
All Indica  2759 48.20% 49.50% 2.36% 0.00% NA
All Japonica  1512 83.20% 11.00% 4.63% 0.00% TA: 1.19%
Aus  269 36.80% 60.20% 2.97% 0.00% NA
Indica I  595 59.00% 38.00% 3.03% 0.00% NA
Indica II  465 50.30% 47.30% 2.37% 0.00% NA
Indica III  913 39.10% 59.80% 1.10% 0.00% NA
Indica Intermediate  786 49.20% 47.50% 3.31% 0.00% NA
Temperate Japonica  767 86.60% 4.00% 7.04% 0.00% TA: 2.35%
Tropical Japonica  504 77.00% 21.60% 1.39% 0.00% NA
Japonica Intermediate  241 85.50% 10.80% 3.73% 0.00% NA
VI/Aromatic  96 81.20% 16.70% 2.08% 0.00% NA
Intermediate  90 64.40% 32.20% 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
vg0222065930 T -> A LOC_Os02g36530.1 upstream_gene_variant ; 435.0bp to feature; MODIFIER silent_mutation Average:99.201; most accessible tissue: Zhenshan97 flag leaf, score: 99.943 N N N N
vg0222065930 T -> A LOC_Os02g36520.1 downstream_gene_variant ; 1754.0bp to feature; MODIFIER silent_mutation Average:99.201; most accessible tissue: Zhenshan97 flag leaf, score: 99.943 N N N N
vg0222065930 T -> A LOC_Os02g36550.1 downstream_gene_variant ; 2084.0bp to feature; MODIFIER silent_mutation Average:99.201; most accessible tissue: Zhenshan97 flag leaf, score: 99.943 N N N N
vg0222065930 T -> A LOC_Os02g36540.1 intron_variant ; MODIFIER silent_mutation Average:99.201; most accessible tissue: Zhenshan97 flag leaf, score: 99.943 N N N N
vg0222065930 T -> TA LOC_Os02g36530.1 upstream_gene_variant ; 436.0bp to feature; MODIFIER silent_mutation Average:99.201; most accessible tissue: Zhenshan97 flag leaf, score: 99.943 N N N N
vg0222065930 T -> TA LOC_Os02g36520.1 downstream_gene_variant ; 1755.0bp to feature; MODIFIER silent_mutation Average:99.201; most accessible tissue: Zhenshan97 flag leaf, score: 99.943 N N N N
vg0222065930 T -> TA LOC_Os02g36550.1 downstream_gene_variant ; 2083.0bp to feature; MODIFIER silent_mutation Average:99.201; most accessible tissue: Zhenshan97 flag leaf, score: 99.943 N N N N
vg0222065930 T -> TA LOC_Os02g36540.1 intron_variant ; MODIFIER silent_mutation Average:99.201; most accessible tissue: Zhenshan97 flag leaf, score: 99.943 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)
vg0222065930 T A -0.01 0.0 0.0 0.0 0.0 -0.01
vg0222065930 T TA 0.0 0.02 -0.11 -0.08 -0.05 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0222065930 1.26E-06 4.55E-07 mr1095 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
vg0222065930 6.92E-06 NA mr1101 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
vg0222065930 7.27E-08 7.27E-08 mr1589 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