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Detailed information for vg0919019906:

Variant ID: vg0919019906 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 19019906
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGCAAGAGAAGAAATATCTACTTGTCCCTCACACATACTCTCTCCATTAAAAAAAAAGACAATCTAGAGGATCGTCTCGGATTGTCTCTTCCTAGTACAA[C/T]
GAATTTAAACAACACTTTATCCAGATTTGTTATGAAGGGGTCACATTTTTTTCTAGATTTTTTTTTCCTGAGGAGTCATAATATATTATCCAAGAATGCT

Reverse complement sequence

AGCATTCTTGGATAATATATTATGACTCCTCAGGAAAAAAAAATCTAGAAAAAAATGTGACCCCTTCATAACAAATCTGGATAAAGTGTTGTTTAAATTC[G/A]
TTGTACTAGGAAGAGACAATCCGAGACGATCCTCTAGATTGTCTTTTTTTTTAATGGAGAGAGTATGTGTGAGGGACAAGTAGATATTTCTTCTCTTGCC

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 39.50% 4.10% 8.51% 47.97% NA
All Indica  2759 10.80% 0.40% 13.16% 75.68% NA
All Japonica  1512 88.10% 11.80% 0.13% 0.00% NA
Aus  269 29.00% 0.00% 11.90% 59.11% NA
Indica I  595 7.90% 0.00% 22.35% 69.75% NA
Indica II  465 12.90% 0.00% 5.59% 81.51% NA
Indica III  913 9.40% 1.00% 11.61% 77.98% NA
Indica Intermediate  786 13.40% 0.10% 12.47% 74.05% NA
Temperate Japonica  767 99.50% 0.40% 0.13% 0.00% NA
Tropical Japonica  504 73.60% 26.40% 0.00% 0.00% NA
Japonica Intermediate  241 82.20% 17.40% 0.41% 0.00% NA
VI/Aromatic  96 96.90% 0.00% 1.04% 2.08% NA
Intermediate  90 71.10% 4.40% 4.44% 20.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0919019906 C -> DEL N N silent_mutation Average:74.188; most accessible tissue: Minghui63 flag leaf, score: 93.631 N N N N
vg0919019906 C -> T LOC_Os09g31506.1 upstream_gene_variant ; 1152.0bp to feature; MODIFIER silent_mutation Average:74.188; most accessible tissue: Minghui63 flag leaf, score: 93.631 N N N N
vg0919019906 C -> T LOC_Os09g31514.1 downstream_gene_variant ; 514.0bp to feature; MODIFIER silent_mutation Average:74.188; most accessible tissue: Minghui63 flag leaf, score: 93.631 N N N N
vg0919019906 C -> T LOC_Os09g31514.2 downstream_gene_variant ; 514.0bp to feature; MODIFIER silent_mutation Average:74.188; most accessible tissue: Minghui63 flag leaf, score: 93.631 N N N N
vg0919019906 C -> T LOC_Os09g31514.4 downstream_gene_variant ; 514.0bp to feature; MODIFIER silent_mutation Average:74.188; most accessible tissue: Minghui63 flag leaf, score: 93.631 N N N N
vg0919019906 C -> T LOC_Os09g31514.3 downstream_gene_variant ; 2230.0bp to feature; MODIFIER silent_mutation Average:74.188; most accessible tissue: Minghui63 flag leaf, score: 93.631 N N N N
vg0919019906 C -> T LOC_Os09g31506-LOC_Os09g31514 intergenic_region ; MODIFIER silent_mutation Average:74.188; most accessible tissue: Minghui63 flag leaf, score: 93.631 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)
vg0919019906 C T -0.04 -0.11 -0.08 -0.05 -0.07 -0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0919019906 NA 3.17E-09 mr1022 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
vg0919019906 NA 9.73E-06 mr1225 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
vg0919019906 NA 5.15E-06 mr1232_2 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
vg0919019906 NA 9.35E-07 mr1557_2 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
vg0919019906 NA 3.50E-07 mr1905_2 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
vg0919019906 NA 3.61E-07 mr1944_2 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