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Detailed information for vg0432144497:

Variant ID: vg0432144497 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 32144497
Reference Allele: CAlternative Allele: G
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.90, G: 0.11, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:


GGGAACTGTTCCTAATCGAGTGATTAGCATTAACTAAATTGGCTAATCACGTGGATTGACAGCCTTAAAATAGGGTGCTGGTATTAGGCTTCGACGTCAC[C/G]
GCCTGATCCTTGAATGTTTTTTACTGCTTGTAGTATAGTTGCTGCAGCTGAGATTCCATTTCTGATCTGAACATCTAGCATTTCACATTTCTAATCCAAG

Reverse complement sequence

CTTGGATTAGAAATGTGAAATGCTAGATGTTCAGATCAGAAATGGAATCTCAGCTGCAGCAACTATACTACAAGCAGTAAAAAACATTCAAGGATCAGGC[G/C]
GTGACGTCGAAGCCTAATACCAGCACCCTATTTTAAGGCTGTCAATCCACGTGATTAGCCAATTTAGTTAATGCTAATCACTCGATTAGGAACAGTTCCC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 51.20% 35.10% 10.26% 3.34% NA
All Indica  2759 32.20% 46.10% 16.02% 5.65% NA
All Japonica  1512 85.80% 12.00% 2.05% 0.07% NA
Aus  269 38.30% 60.20% 1.49% 0.00% NA
Indica I  595 24.90% 66.60% 7.56% 1.01% NA
Indica II  465 36.80% 27.30% 25.16% 10.75% NA
Indica III  913 35.60% 39.30% 18.07% 7.01% NA
Indica Intermediate  786 31.00% 49.70% 14.63% 4.58% NA
Temperate Japonica  767 98.20% 1.80% 0.00% 0.00% NA
Tropical Japonica  504 64.10% 29.80% 5.95% 0.20% NA
Japonica Intermediate  241 92.10% 7.50% 0.41% 0.00% NA
VI/Aromatic  96 76.00% 24.00% 0.00% 0.00% NA
Intermediate  90 66.70% 23.30% 8.89% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0432144497 C -> DEL N N silent_mutation Average:85.531; most accessible tissue: Zhenshan97 panicle, score: 99.696 N N N N
vg0432144497 C -> G LOC_Os04g53940.1 upstream_gene_variant ; 2856.0bp to feature; MODIFIER silent_mutation Average:85.531; most accessible tissue: Zhenshan97 panicle, score: 99.696 N N N N
vg0432144497 C -> G LOC_Os04g53950.1 upstream_gene_variant ; 1182.0bp to feature; MODIFIER silent_mutation Average:85.531; most accessible tissue: Zhenshan97 panicle, score: 99.696 N N N N
vg0432144497 C -> G LOC_Os04g53950.2 upstream_gene_variant ; 1182.0bp to feature; MODIFIER silent_mutation Average:85.531; most accessible tissue: Zhenshan97 panicle, score: 99.696 N N N N
vg0432144497 C -> G LOC_Os04g53950.3 upstream_gene_variant ; 1190.0bp to feature; MODIFIER silent_mutation Average:85.531; most accessible tissue: Zhenshan97 panicle, score: 99.696 N N N N
vg0432144497 C -> G LOC_Os04g53930.1 downstream_gene_variant ; 3314.0bp to feature; MODIFIER silent_mutation Average:85.531; most accessible tissue: Zhenshan97 panicle, score: 99.696 N N N N
vg0432144497 C -> G LOC_Os04g53930.2 downstream_gene_variant ; 3314.0bp to feature; MODIFIER silent_mutation Average:85.531; most accessible tissue: Zhenshan97 panicle, score: 99.696 N N N N
vg0432144497 C -> G LOC_Os04g53940-LOC_Os04g53950 intergenic_region ; MODIFIER silent_mutation Average:85.531; most accessible tissue: Zhenshan97 panicle, score: 99.696 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)
vg0432144497 C G -0.05 -0.05 -0.03 0.01 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0432144497 NA 4.46E-08 mr1265_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
vg0432144497 9.58E-07 1.43E-07 mr1265_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
vg0432144497 6.25E-06 1.10E-09 mr1528_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
vg0432144497 1.79E-06 1.09E-06 mr1528_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