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Detailed information for vg0609042750:

Variant ID: vg0609042750 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 9042750
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

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

Flanking Sequence (100 bp) in Reference Genome:


GGCTGTTGACATGTCATATACTGTGCTGACAAATTTGTCCTAATTAATGAAAAATTTCTTGTTTTGACCGGTTACTCGGTTGGATCTCTGATGAGTGGCC[C/T]
AAATTGGTTTTCCAAGGTTTTGACATGGAAAGTCTTCTAGAGGAACCACACAAGTCCATCTCAAAAATTAATGGTGCCCTAGCCTTCGCACTTCTCTCCC

Reverse complement sequence

GGGAGAGAAGTGCGAAGGCTAGGGCACCATTAATTTTTGAGATGGACTTGTGTGGTTCCTCTAGAAGACTTTCCATGTCAAAACCTTGGAAAACCAATTT[G/A]
GGCCACTCATCAGAGATCCAACCGAGTAACCGGTCAAAACAAGAAATTTTTCATTAATTAGGACAAATTTGTCAGCACAGTATATGACATGTCAACAGCC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 93.70% 6.30% 0.02% 0.00% NA
All Indica  2759 97.10% 2.90% 0.04% 0.00% NA
All Japonica  1512 91.70% 8.30% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 98.50% 1.50% 0.00% 0.00% NA
Indica III  913 92.00% 7.90% 0.11% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 96.60% 3.40% 0.00% 0.00% NA
Tropical Japonica  504 91.30% 8.70% 0.00% 0.00% NA
Japonica Intermediate  241 76.80% 23.20% 0.00% 0.00% NA
VI/Aromatic  96 12.50% 87.50% 0.00% 0.00% NA
Intermediate  90 91.10% 8.90% 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
vg0609042750 C -> T LOC_Os06g15910.1 upstream_gene_variant ; 4975.0bp to feature; MODIFIER silent_mutation Average:88.01; most accessible tissue: Zhenshan97 flag leaf, score: 97.431 N N N N
vg0609042750 C -> T LOC_Os06g15910-LOC_Os06g15920 intergenic_region ; MODIFIER silent_mutation Average:88.01; most accessible tissue: Zhenshan97 flag leaf, score: 97.431 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)
vg0609042750 C T -0.04 -0.18 -0.12 -0.02 -0.02 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0609042750 NA 6.92E-07 mr1522_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
vg0609042750 NA 9.16E-09 mr1829_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