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Detailed information for vg1128987468:

Variant ID: vg1128987468 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 28987468
Reference Allele: CAlternative Allele: G
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AAACCTTAACGTTTTCATTTGGGGCCACGAGCACGGCCACCGCAACCATATCAGTATCACATTCCATCCCAAATCGCCAAAAAATCCCACCAATCCACTA[C/G]
TATTCCACTCCACCTCGTCCAGGGCAAGATCCACAGGATGGCGTCCTCTGACGACGGCGTCGTGGCCCTCTACGGCGGCGGCAAGGTCTCCTGCAAGCCC

Reverse complement sequence

GGGCTTGCAGGAGACCTTGCCGCCGCCGTAGAGGGCCACGACGCCGTCGTCAGAGGACGCCATCCTGTGGATCTTGCCCTGGACGAGGTGGAGTGGAATA[G/C]
TAGTGGATTGGTGGGATTTTTTGGCGATTTGGGATGGAATGTGATACTGATATGGTTGCGGTGGCCGTGCTCGTGGCCCCAAATGAAAACGTTAAGGTTT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 62.00% 37.70% 0.28% 0.00% NA
All Indica  2759 85.50% 14.20% 0.22% 0.00% NA
All Japonica  1512 17.00% 82.90% 0.13% 0.00% NA
Aus  269 80.70% 18.60% 0.74% 0.00% NA
Indica I  595 89.20% 10.60% 0.17% 0.00% NA
Indica II  465 94.40% 5.20% 0.43% 0.00% NA
Indica III  913 81.10% 18.80% 0.11% 0.00% NA
Indica Intermediate  786 82.70% 17.00% 0.25% 0.00% NA
Temperate Japonica  767 16.00% 84.00% 0.00% 0.00% NA
Tropical Japonica  504 18.10% 81.50% 0.40% 0.00% NA
Japonica Intermediate  241 17.80% 82.20% 0.00% 0.00% NA
VI/Aromatic  96 50.00% 50.00% 0.00% 0.00% NA
Intermediate  90 52.20% 44.40% 3.33% 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
vg1128987468 C -> G LOC_Os11g48080.1 5_prime_UTR_variant ; 38.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg1128987468 C -> G LOC_Os11g48070.1 downstream_gene_variant ; 1705.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg1128987468 C -> G LOC_Os11g48090.5 downstream_gene_variant ; 1963.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg1128987468 C -> G LOC_Os11g48090.3 downstream_gene_variant ; 1963.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg1128987468 C -> G LOC_Os11g48090.4 downstream_gene_variant ; 1963.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg1128987468 C -> G LOC_Os11g48090.2 downstream_gene_variant ; 4021.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 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)
vg1128987468 C G -0.03 -0.04 -0.03 -0.04 -0.04 -0.05

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1128987468 2.00E-06 2.00E-06 mr1601 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
vg1128987468 NA 6.64E-07 mr1418_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
vg1128987468 NA 9.97E-06 mr1419_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
vg1128987468 NA 9.88E-08 mr1683_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
vg1128987468 NA 7.15E-14 mr1838_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