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Detailed information for vg0310177475:

Variant ID: vg0310177475 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 10177475
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:


ACAGAAGAAGATAGCCATGGCCACCGGCCTAGCTCTATTATGCTCCCCTCCTCCATCTCTCCTTTTATTGCTTCCACAGCAGCAGCCTTCTCGTCGCCAC[C/T]
GCCTCTGCCATTCGGACTCGAGTGAAGAGAGCAATTGAGGATGGGGAAGATATGACATGTGGCCCCCATTGTTTTTTTTTCTGATTGGAATGCCACGTAC

Reverse complement sequence

GTACGTGGCATTCCAATCAGAAAAAAAAACAATGGGGGCCACATGTCATATCTTCCCCATCCTCAATTGCTCTCTTCACTCGAGTCCGAATGGCAGAGGC[G/A]
GTGGCGACGAGAAGGCTGCTGCTGTGGAAGCAATAAAAGGAGAGATGGAGGAGGGGAGCATAATAGAGCTAGGCCGGTGGCCATGGCTATCTTCTTCTGT

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 94.40% 5.00% 0.63% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 82.70% 15.30% 1.98% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 72.20% 24.30% 3.52% 0.00% NA
Tropical Japonica  504 97.20% 2.80% 0.00% 0.00% NA
Japonica Intermediate  241 85.90% 12.90% 1.24% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 94.40% 5.60% 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
vg0310177475 C -> T LOC_Os03g18160.1 downstream_gene_variant ; 2961.0bp to feature; MODIFIER silent_mutation Average:67.382; most accessible tissue: Minghui63 young leaf, score: 83.419 N N N N
vg0310177475 C -> T LOC_Os03g18160-LOC_Os03g18170 intergenic_region ; MODIFIER silent_mutation Average:67.382; most accessible tissue: Minghui63 young leaf, score: 83.419 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)
vg0310177475 C T 0.0 -0.01 -0.02 0.0 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0310177475 4.99E-06 NA mr1043 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
vg0310177475 8.69E-07 1.20E-06 mr1185 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
vg0310177475 3.71E-07 3.71E-07 mr1185 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
vg0310177475 4.86E-06 1.23E-06 mr1269 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
vg0310177475 NA 1.19E-08 mr1439 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
vg0310177475 3.97E-07 3.56E-06 mr1479 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
vg0310177475 5.63E-06 5.64E-06 mr1479 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
vg0310177475 NA 1.62E-06 mr1662 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
vg0310177475 1.83E-06 3.66E-07 mr1677 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
vg0310177475 5.36E-06 NA mr1677 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
vg0310177475 3.06E-06 5.08E-06 mr1678 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
vg0310177475 6.78E-07 1.12E-06 mr1975 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