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Detailed information for vg0727958020:

Variant ID: vg0727958020 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 27958020
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.64, T: 0.36, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:


ACTTAAAGTACTATGAGTGATAAAACAACCCATAATAAAATAAATTATAATTACGTAAATTTTTTGAATAAGACGAATGGTCAAACATGTGAGAAAAAGT[C/T]
AACGACGTCATCTATTAAAAAATAGAGGTAGTATTTGACAACTTTAAAAAATAGTATGGTTTGAAATAACATCAGAACAAACCAGTAACTTCAAATTTTT

Reverse complement sequence

AAAAATTTGAAGTTACTGGTTTGTTCTGATGTTATTTCAAACCATACTATTTTTTAAAGTTGTCAAATACTACCTCTATTTTTTAATAGATGACGTCGTT[G/A]
ACTTTTTCTCACATGTTTGACCATTCGTCTTATTCAAAAAATTTACGTAATTATAATTTATTTTATTATGGGTTGTTTTATCACTCATAGTACTTTAAGT

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 60.60% 22.10% 10.35% 6.98% NA
All Indica  2759 39.60% 31.90% 16.78% 11.71% NA
All Japonica  1512 96.20% 3.20% 0.33% 0.26% NA
Aus  269 79.60% 15.60% 4.83% 0.00% NA
Indica I  595 58.20% 6.70% 23.53% 11.60% NA
Indica II  465 29.70% 46.00% 16.13% 8.17% NA
Indica III  913 28.60% 42.20% 13.58% 15.66% NA
Indica Intermediate  786 44.30% 30.70% 15.78% 9.29% NA
Temperate Japonica  767 98.80% 0.40% 0.26% 0.52% NA
Tropical Japonica  504 91.90% 7.70% 0.40% 0.00% NA
Japonica Intermediate  241 96.70% 2.90% 0.41% 0.00% NA
VI/Aromatic  96 40.60% 57.30% 2.08% 0.00% NA
Intermediate  90 70.00% 20.00% 6.67% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0727958020 C -> DEL N N silent_mutation Average:82.948; most accessible tissue: Minghui63 flag leaf, score: 95.88 N N N N
vg0727958020 C -> T LOC_Os07g46780.1 upstream_gene_variant ; 533.0bp to feature; MODIFIER silent_mutation Average:82.948; most accessible tissue: Minghui63 flag leaf, score: 95.88 N N N N
vg0727958020 C -> T LOC_Os07g46790.1 upstream_gene_variant ; 2420.0bp to feature; MODIFIER silent_mutation Average:82.948; most accessible tissue: Minghui63 flag leaf, score: 95.88 N N N N
vg0727958020 C -> T LOC_Os07g46780.2 upstream_gene_variant ; 539.0bp to feature; MODIFIER silent_mutation Average:82.948; most accessible tissue: Minghui63 flag leaf, score: 95.88 N N N N
vg0727958020 C -> T LOC_Os07g46780.3 upstream_gene_variant ; 539.0bp to feature; MODIFIER silent_mutation Average:82.948; most accessible tissue: Minghui63 flag leaf, score: 95.88 N N N N
vg0727958020 C -> T LOC_Os07g46780-LOC_Os07g46790 intergenic_region ; MODIFIER silent_mutation Average:82.948; most accessible tissue: Minghui63 flag leaf, score: 95.88 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)
vg0727958020 C T 0.02 0.05 0.05 0.02 0.04 0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0727958020 NA 7.68E-07 mr1032 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
vg0727958020 NA 6.39E-08 mr1165 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
vg0727958020 2.86E-06 NA mr1460 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
vg0727958020 4.49E-06 4.49E-06 mr1460 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
vg0727958020 NA 1.22E-07 mr1478 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
vg0727958020 NA 1.29E-06 mr1502 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
vg0727958020 1.05E-07 NA mr1457_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
vg0727958020 2.11E-09 1.57E-10 mr1457_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