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Detailed information for vg0315642911:

Variant ID: vg0315642911 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 15642911
Reference Allele: CAlternative Allele: A
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 304. )

Flanking Sequence (100 bp) in Reference Genome:


TTGTGCGTTTGTTAAAACCCTACGCTCCAGTCCAACCAAGCCAAAGGACTAATTCGGTTTAAACAACTCTCTTTGCCGACTGACAGATCAGGTAAGATGG[C/A]
TGATCGGATACACGGGATAGTCTCCAATCTCATGAAAATGTAGAGAATGGTTTTGAAAATTTTCGAGACGTTAGGTTTTACAATACTACTCCCTCCATCC

Reverse complement sequence

GGATGGAGGGAGTAGTATTGTAAAACCTAACGTCTCGAAAATTTTCAAAACCATTCTCTACATTTTCATGAGATTGGAGACTATCCCGTGTATCCGATCA[G/T]
CCATCTTACCTGATCTGTCAGTCGGCAAAGAGAGTTGTTTAAACCGAATTAGTCCTTTGGCTTGGTTGGACTGGAGCGTAGGGTTTTAACAAACGCACAA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 79.80% 19.20% 1.04% 0.00% NA
All Indica  2759 99.30% 0.40% 0.25% 0.00% NA
All Japonica  1512 47.20% 50.30% 2.58% 0.00% NA
Aus  269 81.40% 18.60% 0.00% 0.00% NA
Indica I  595 99.80% 0.00% 0.17% 0.00% NA
Indica II  465 99.10% 0.90% 0.00% 0.00% NA
Indica III  913 99.90% 0.00% 0.11% 0.00% NA
Indica Intermediate  786 98.50% 0.90% 0.64% 0.00% NA
Temperate Japonica  767 13.00% 83.60% 3.39% 0.00% NA
Tropical Japonica  504 90.70% 9.10% 0.20% 0.00% NA
Japonica Intermediate  241 64.70% 30.30% 4.98% 0.00% NA
VI/Aromatic  96 24.00% 75.00% 1.04% 0.00% NA
Intermediate  90 82.20% 15.60% 2.22% 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
vg0315642911 C -> A LOC_Os03g27310.1 upstream_gene_variant ; 2694.0bp to feature; MODIFIER silent_mutation Average:81.922; most accessible tissue: Minghui63 root, score: 87.044 N N N N
vg0315642911 C -> A LOC_Os03g27310.2 upstream_gene_variant ; 4180.0bp to feature; MODIFIER silent_mutation Average:81.922; most accessible tissue: Minghui63 root, score: 87.044 N N N N
vg0315642911 C -> A LOC_Os03g27290.1 downstream_gene_variant ; 375.0bp to feature; MODIFIER silent_mutation Average:81.922; most accessible tissue: Minghui63 root, score: 87.044 N N N N
vg0315642911 C -> A LOC_Os03g27300.1 downstream_gene_variant ; 1305.0bp to feature; MODIFIER silent_mutation Average:81.922; most accessible tissue: Minghui63 root, score: 87.044 N N N N
vg0315642911 C -> A LOC_Os03g27290-LOC_Os03g27300 intergenic_region ; MODIFIER silent_mutation Average:81.922; most accessible tissue: Minghui63 root, score: 87.044 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)
vg0315642911 C A -0.07 -0.02 -0.01 -0.02 -0.03 -0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0315642911 NA 8.32E-14 Grain_length Jap_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0315642911 4.47E-08 NA mr1113_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
vg0315642911 5.48E-07 NA mr1117_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
vg0315642911 6.68E-06 NA mr1119_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
vg0315642911 1.89E-06 NA mr1120_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
vg0315642911 NA 2.54E-07 mr1310_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
vg0315642911 3.51E-06 NA mr1496_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