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Detailed information for vg0721047449:

Variant ID: vg0721047449 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 21047449
Reference Allele: TAlternative Allele: G
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.97, G: 0.03, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:


TACAGTCGATTTTTGACCAAAATGTGTGAATGGTTGTCGCTATATATGCTAATAATCTGCGGCATCATAGTTGCTGTCCCTATTGTTTAGCAGTCAATGT[T/G]
GACGAAAATGCGGATGACTTGGTGATGCTAACATGCATGATTATTATTTGCTTTGTCTGTTCGTGTTTTCAGGGTGAGTTGTCTGATGGAGCCGAGATTG

Reverse complement sequence

CAATCTCGGCTCCATCAGACAACTCACCCTGAAAACACGAACAGACAAAGCAAATAATAATCATGCATGTTAGCATCACCAAGTCATCCGCATTTTCGTC[A/C]
ACATTGACTGCTAAACAATAGGGACAGCAACTATGATGCCGCAGATTATTAGCATATATAGCGACAACCATTCACACATTTTGGTCAAAAATCGACTGTA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 50.70% 49.20% 0.13% 0.00% NA
All Indica  2759 27.90% 71.80% 0.22% 0.00% NA
All Japonica  1512 84.30% 15.70% 0.00% 0.00% NA
Aus  269 91.10% 8.90% 0.00% 0.00% NA
Indica I  595 12.40% 87.20% 0.34% 0.00% NA
Indica II  465 20.00% 80.00% 0.00% 0.00% NA
Indica III  913 46.20% 53.50% 0.33% 0.00% NA
Indica Intermediate  786 23.20% 76.70% 0.13% 0.00% NA
Temperate Japonica  767 98.80% 1.20% 0.00% 0.00% NA
Tropical Japonica  504 59.70% 40.30% 0.00% 0.00% NA
Japonica Intermediate  241 89.20% 10.80% 0.00% 0.00% NA
VI/Aromatic  96 63.50% 36.50% 0.00% 0.00% NA
Intermediate  90 51.10% 48.90% 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
vg0721047449 T -> G LOC_Os07g35130.1 downstream_gene_variant ; 4056.0bp to feature; MODIFIER silent_mutation Average:84.557; most accessible tissue: Callus, score: 98.397 N N N N
vg0721047449 T -> G LOC_Os07g35150.1 downstream_gene_variant ; 3679.0bp to feature; MODIFIER silent_mutation Average:84.557; most accessible tissue: Callus, score: 98.397 N N N N
vg0721047449 T -> G LOC_Os07g35140.1 intron_variant ; MODIFIER silent_mutation Average:84.557; most accessible tissue: Callus, score: 98.397 N N N N
vg0721047449 T -> G LOC_Os07g35140.2 intron_variant ; MODIFIER silent_mutation Average:84.557; most accessible tissue: Callus, score: 98.397 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)
vg0721047449 T G 0.02 0.09 0.07 0.05 0.06 0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0721047449 NA 9.06E-06 mr1082 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
vg0721047449 NA 3.44E-07 mr1083 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
vg0721047449 NA 6.54E-06 mr1226 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
vg0721047449 NA 3.43E-07 mr1121_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
vg0721047449 3.99E-06 6.69E-08 mr1220_2 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
vg0721047449 NA 7.10E-06 mr1691_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
vg0721047449 NA 1.65E-14 mr1807_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
vg0721047449 NA 4.74E-06 mr1896_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
vg0721047449 NA 1.86E-06 mr1936_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