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Detailed information for vg0915918134:

Variant ID: vg0915918134 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 15918134
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, T: 0.04, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:


GGCCAGCAGCAACCAGCAGGGAGAAAGCAATCAGCAGCACTCCATTCATCAGGAGGCACGCAACACCAAAGCACAGCAAACAGCACGTTAGCAAACAGCA[C/T]
TATAGTAGGTTCTCAACTTCTCATCTGCTTCTCTCTTTCTCCTCCCTAACAGTAGGGTTTTTTTTTCTTTAGGTTTAAATGTTCAATCTCATTTCAATTT

Reverse complement sequence

AAATTGAAATGAGATTGAACATTTAAACCTAAAGAAAAAAAAACCCTACTGTTAGGGAGGAGAAAGAGAGAAGCAGATGAGAAGTTGAGAACCTACTATA[G/A]
TGCTGTTTGCTAACGTGCTGTTTGCTGTGCTTTGGTGTTGCGTGCCTCCTGATGAATGGAGTGCTGCTGATTGCTTTCTCCCTGCTGGTTGCTGCTGGCC

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 51.30% 48.40% 0.08% 0.21% NA
All Indica  2759 25.30% 74.20% 0.14% 0.36% NA
All Japonica  1512 99.30% 0.70% 0.00% 0.00% NA
Aus  269 23.40% 76.60% 0.00% 0.00% NA
Indica I  595 5.00% 93.80% 0.00% 1.18% NA
Indica II  465 56.80% 43.20% 0.00% 0.00% NA
Indica III  913 17.90% 81.80% 0.33% 0.00% NA
Indica Intermediate  786 30.50% 69.00% 0.13% 0.38% NA
Temperate Japonica  767 99.50% 0.50% 0.00% 0.00% NA
Tropical Japonica  504 99.20% 0.80% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 74.40% 25.60% 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
vg0915918134 C -> DEL N N silent_mutation Average:90.698; most accessible tissue: Zhenshan97 panicle, score: 96.414 N N N N
vg0915918134 C -> T LOC_Os09g26330.1 upstream_gene_variant ; 3106.0bp to feature; MODIFIER silent_mutation Average:90.698; most accessible tissue: Zhenshan97 panicle, score: 96.414 N N N N
vg0915918134 C -> T LOC_Os09g26350.1 upstream_gene_variant ; 510.0bp to feature; MODIFIER silent_mutation Average:90.698; most accessible tissue: Zhenshan97 panicle, score: 96.414 N N N N
vg0915918134 C -> T LOC_Os09g26340.1 downstream_gene_variant ; 1108.0bp to feature; MODIFIER silent_mutation Average:90.698; most accessible tissue: Zhenshan97 panicle, score: 96.414 N N N N
vg0915918134 C -> T LOC_Os09g26360.1 downstream_gene_variant ; 3494.0bp to feature; MODIFIER silent_mutation Average:90.698; most accessible tissue: Zhenshan97 panicle, score: 96.414 N N N N
vg0915918134 C -> T LOC_Os09g26350-LOC_Os09g26360 intergenic_region ; MODIFIER silent_mutation Average:90.698; most accessible tissue: Zhenshan97 panicle, score: 96.414 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)
vg0915918134 C T 0.01 -0.02 -0.03 -0.03 -0.03 -0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0915918134 NA 2.45E-06 mr1425 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
vg0915918134 NA 2.19E-10 mr1904 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
vg0915918134 NA 4.52E-10 mr1050_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
vg0915918134 NA 4.02E-07 mr1272_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
vg0915918134 NA 1.07E-07 mr1607_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
vg0915918134 NA 1.59E-09 mr1835_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
vg0915918134 NA 7.29E-06 mr1895_2 Ind_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
vg0915918134 NA 2.64E-18 mr1904_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
vg0915918134 NA 1.15E-07 mr1904_2 Ind_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