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Detailed information for vg0418759478:

Variant ID: vg0418759478 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 18759478
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.98, G: 0.02, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:


TTTTTTGATATCGTACTCTGGTACTGTATATGTACAGCATGATGTTAATAATCTGTGTGTGGGTTTGTGCGCTTATTTCCATATCTATAAGCAGTTGTGC[G/A]
CTCGTTATCAATTAAGGTGCTTTGTACAATTGTGTGCTGGCTAGCTAGCTGCTGCTACTTTATCATGCATTTTCATAGAGATATCTCTTGTACTTCTTTT

Reverse complement sequence

AAAAGAAGTACAAGAGATATCTCTATGAAAATGCATGATAAAGTAGCAGCAGCTAGCTAGCCAGCACACAATTGTACAAAGCACCTTAATTGATAACGAG[C/T]
GCACAACTGCTTATAGATATGGAAATAAGCGCACAAACCCACACACAGATTATTAACATCATGCTGTACATATACAGTACCAGAGTACGATATCAAAAAA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 53.50% 46.30% 0.15% 0.00% NA
All Indica  2759 82.40% 17.40% 0.25% 0.00% NA
All Japonica  1512 4.10% 95.90% 0.00% 0.00% NA
Aus  269 61.70% 38.30% 0.00% 0.00% NA
Indica I  595 77.80% 22.00% 0.17% 0.00% NA
Indica II  465 58.30% 41.30% 0.43% 0.00% NA
Indica III  913 98.10% 1.80% 0.11% 0.00% NA
Indica Intermediate  786 81.80% 17.80% 0.38% 0.00% NA
Temperate Japonica  767 1.60% 98.40% 0.00% 0.00% NA
Tropical Japonica  504 3.20% 96.80% 0.00% 0.00% NA
Japonica Intermediate  241 14.10% 85.90% 0.00% 0.00% NA
VI/Aromatic  96 8.30% 91.70% 0.00% 0.00% NA
Intermediate  90 23.30% 76.70% 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
vg0418759478 G -> A LOC_Os04g31350.1 upstream_gene_variant ; 630.0bp to feature; MODIFIER silent_mutation Average:57.153; most accessible tissue: Zhenshan97 flower, score: 97.094 N N N N
vg0418759478 G -> A LOC_Os04g31360.1 downstream_gene_variant ; 1712.0bp to feature; MODIFIER silent_mutation Average:57.153; most accessible tissue: Zhenshan97 flower, score: 97.094 N N N N
vg0418759478 G -> A LOC_Os04g31350-LOC_Os04g31360 intergenic_region ; MODIFIER silent_mutation Average:57.153; most accessible tissue: Zhenshan97 flower, score: 97.094 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)
vg0418759478 G A 0.03 0.02 0.0 0.02 0.02 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0418759478 6.83E-06 4.75E-14 mr1521 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
vg0418759478 4.82E-06 4.82E-06 mr1521 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
vg0418759478 2.68E-06 4.45E-11 mr1851 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
vg0418759478 6.92E-11 8.24E-14 mr1851 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
vg0418759478 NA 6.44E-13 mr1864 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
vg0418759478 2.34E-09 1.54E-12 mr1864 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
vg0418759478 NA 8.17E-10 mr1349_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
vg0418759478 7.10E-06 2.14E-14 mr1521_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
vg0418759478 3.74E-07 4.08E-06 mr1521_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
vg0418759478 NA 9.28E-06 mr1726_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