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Detailed information for vg0824524218:

Variant ID: vg0824524218 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 24524218
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.93, T: 0.06, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:


AGTTAAGGAGGCAACTACGTACTACCTCCGTCCCATAAAAATTAAATTTAAAACCATATATGATATATTCTAATACAATGAATCTGAACGGATATATGTC[C/T]
AGATTCGTAGTTCTAAGATGTGTCACATTTAGTACTAGGTTGGTTTTTATGGAACGGAGAGAGTACGTGACTACTGAGGAGTCCGGACAGGCGTCCGATT

Reverse complement sequence

AATCGGACGCCTGTCCGGACTCCTCAGTAGTCACGTACTCTCTCCGTTCCATAAAAACCAACCTAGTACTAAATGTGACACATCTTAGAACTACGAATCT[G/A]
GACATATATCCGTTCAGATTCATTGTATTAGAATATATCATATATGGTTTTAAATTTAATTTTTATGGGACGGAGGTAGTACGTAGTTGCCTCCTTAACT

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 62.80% 35.90% 1.29% 0.00% NA
All Indica  2759 72.60% 26.60% 0.80% 0.00% NA
All Japonica  1512 40.00% 57.80% 2.18% 0.00% NA
Aus  269 95.50% 3.30% 1.12% 0.00% NA
Indica I  595 87.20% 11.60% 1.18% 0.00% NA
Indica II  465 79.40% 19.80% 0.86% 0.00% NA
Indica III  913 56.40% 43.20% 0.44% 0.00% NA
Indica Intermediate  786 76.50% 22.60% 0.89% 0.00% NA
Temperate Japonica  767 14.20% 82.70% 3.13% 0.00% NA
Tropical Japonica  504 80.40% 18.70% 0.99% 0.00% NA
Japonica Intermediate  241 37.80% 60.60% 1.66% 0.00% NA
VI/Aromatic  96 50.00% 50.00% 0.00% 0.00% NA
Intermediate  90 58.90% 37.80% 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
vg0824524218 C -> T LOC_Os08g38790.1 upstream_gene_variant ; 1159.0bp to feature; MODIFIER silent_mutation Average:81.637; most accessible tissue: Zhenshan97 flower, score: 98.073 N N N N
vg0824524218 C -> T LOC_Os08g38800.1 upstream_gene_variant ; 343.0bp to feature; MODIFIER silent_mutation Average:81.637; most accessible tissue: Zhenshan97 flower, score: 98.073 N N N N
vg0824524218 C -> T LOC_Os08g38790-LOC_Os08g38800 intergenic_region ; MODIFIER silent_mutation Average:81.637; most accessible tissue: Zhenshan97 flower, score: 98.073 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)
vg0824524218 C T -0.04 -0.02 -0.02 -0.04 -0.01 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0824524218 NA 1.70E-06 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
vg0824524218 NA 9.37E-08 mr1271 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
vg0824524218 NA 9.49E-06 mr1554 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
vg0824524218 NA 1.48E-08 mr1864 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
vg0824524218 NA 1.70E-08 mr1295_2 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