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Detailed information for vg0602909111:

Variant ID: vg0602909111 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 2909111
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.88, T: 0.12, others allele: 0.00, population size: 69. )

Flanking Sequence (100 bp) in Reference Genome:


ACTACCCTACTTAAGCAAACTGCTCATTCACTGGCACAAAACTGAGGAATCTTGCTACGGCTCACATGGCCCCCTGTCTCCCTCGTGCACAAATTTTTTT[A/T]
AAAAAAATCCAAATCACGTTGCAACGTACGGGCAATATATACGTAGACTGTGTTTAGTTCACACTGAAGTTTAGAAGTTTTGGTTAAAATTGATACGATG

Reverse complement sequence

CATCGTATCAATTTTAACCAAAACTTCTAAACTTCAGTGTGAACTAAACACAGTCTACGTATATATTGCCCGTACGTTGCAACGTGATTTGGATTTTTTT[T/A]
AAAAAAATTTGTGCACGAGGGAGACAGGGGGCCATGTGAGCCGTAGCAAGATTCCTCAGTTTTGTGCCAGTGAATGAGCAGTTTGCTTAAGTAGGGTAGT

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 92.80% 6.10% 1.08% 0.00% NA
All Indica  2759 95.90% 3.80% 0.29% 0.00% NA
All Japonica  1512 91.00% 6.30% 2.65% 0.00% NA
Aus  269 71.70% 27.90% 0.37% 0.00% NA
Indica I  595 92.10% 7.10% 0.84% 0.00% NA
Indica II  465 99.10% 0.60% 0.22% 0.00% NA
Indica III  913 98.40% 1.60% 0.00% 0.00% NA
Indica Intermediate  786 94.10% 5.60% 0.25% 0.00% NA
Temperate Japonica  767 85.50% 10.70% 3.78% 0.00% NA
Tropical Japonica  504 96.60% 2.20% 1.19% 0.00% NA
Japonica Intermediate  241 96.70% 1.20% 2.07% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 88.90% 8.90% 2.22% 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
vg0602909111 A -> T LOC_Os06g06280.1 downstream_gene_variant ; 1807.0bp to feature; MODIFIER silent_mutation Average:87.868; most accessible tissue: Minghui63 panicle, score: 96.383 N N N N
vg0602909111 A -> T LOC_Os06g06280.2 downstream_gene_variant ; 1805.0bp to feature; MODIFIER silent_mutation Average:87.868; most accessible tissue: Minghui63 panicle, score: 96.383 N N N N
vg0602909111 A -> T LOC_Os06g06290.1 intron_variant ; MODIFIER silent_mutation Average:87.868; most accessible tissue: Minghui63 panicle, score: 96.383 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)
vg0602909111 A T 0.03 0.01 0.01 0.01 0.02 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0602909111 NA 1.34E-07 mr1157 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
vg0602909111 NA 4.42E-08 mr1446 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
vg0602909111 NA 1.78E-07 mr1612_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
vg0602909111 1.95E-06 NA mr1720_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