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Detailed information for vg0918217541:

Variant ID: vg0918217541 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 18217541
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, T: 0.02, others allele: 0.00, population size: 204. )

Flanking Sequence (100 bp) in Reference Genome:


GAGGATTACCAGAATTCAGCCCGGCGAAAATGATAATTCAGAATTCAGAAACAATCAGGAAAGTACATGCATGAACCACCAACTGCCCAAATGTAGTACA[G/T]
AGAAGTACAGTGGAAGAATTTTTGACAAGTCTTGATCCGTATGTATATGTACGAACAACTCAACACCTGTGAGCATGTATGCTTATATTTACAAAACAAA

Reverse complement sequence

TTTGTTTTGTAAATATAAGCATACATGCTCACAGGTGTTGAGTTGTTCGTACATATACATACGGATCAAGACTTGTCAAAAATTCTTCCACTGTACTTCT[C/A]
TGTACTACATTTGGGCAGTTGGTGGTTCATGCATGTACTTTCCTGATTGTTTCTGAATTCTGAATTATCATTTTCGCCGGGCTGAATTCTGGTAATCCTC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 86.80% 13.00% 0.21% 0.00% NA
All Indica  2759 90.00% 9.60% 0.36% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 6.70% 93.30% 0.00% 0.00% NA
Indica I  595 90.10% 9.40% 0.50% 0.00% NA
Indica II  465 92.50% 7.10% 0.43% 0.00% NA
Indica III  913 92.40% 7.30% 0.22% 0.00% NA
Indica Intermediate  786 85.60% 14.00% 0.38% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.40% 0.60% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 21.90% 78.10% 0.00% 0.00% NA
Intermediate  90 81.10% 18.90% 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
vg0918217541 G -> T LOC_Os09g29940.1 3_prime_UTR_variant ; 302.0bp to feature; MODIFIER silent_mutation Average:79.1; most accessible tissue: Callus, score: 87.994 N N N N
vg0918217541 G -> T LOC_Os09g29940.2 3_prime_UTR_variant ; 302.0bp to feature; MODIFIER silent_mutation Average:79.1; most accessible tissue: Callus, score: 87.994 N N N N
vg0918217541 G -> T LOC_Os09g29930.1 downstream_gene_variant ; 2433.0bp to feature; MODIFIER silent_mutation Average:79.1; most accessible tissue: Callus, score: 87.994 N N N N
vg0918217541 G -> T LOC_Os09g29930.3 downstream_gene_variant ; 4317.0bp to feature; MODIFIER silent_mutation Average:79.1; most accessible tissue: Callus, score: 87.994 N N N N
vg0918217541 G -> T LOC_Os09g29930.2 downstream_gene_variant ; 2433.0bp to feature; MODIFIER silent_mutation Average:79.1; most accessible tissue: Callus, score: 87.994 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)
vg0918217541 G T -0.09 -0.14 -0.11 -0.1 -0.13 -0.1

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0918217541 NA 2.71E-12 mr1409 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
vg0918217541 NA 4.30E-24 mr1586 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
vg0918217541 NA 1.86E-10 mr1047_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
vg0918217541 3.95E-06 2.67E-06 mr1047_2 Ind_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
vg0918217541 NA 3.58E-07 mr1344_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
vg0918217541 NA 1.13E-07 mr1510_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
vg0918217541 NA 4.54E-08 mr1707_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
vg0918217541 NA 8.95E-06 mr1743_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
vg0918217541 NA 1.96E-12 mr1803_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