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Detailed information for vg0722260306:

Variant ID: vg0722260306 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 22260306
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 322. )

Flanking Sequence (100 bp) in Reference Genome:


GCCGTTTGATTTAACACTTGATTTGATGAGATTCGATAAAATGCCATCTATTTCATTGCCATCTCTATTTTTATACTTTGAAGGGCTTAAGTTATTTATT[G/A]
GCACAAAACTAACCGCGTGAAAGGACTATTTTGTCCCTAACTCTAGAGGTCTCTCTTATGTCAATTTGTTTGTCGCTCTATGAGCTCGCTGACGTCGAGG

Reverse complement sequence

CCTCGACGTCAGCGAGCTCATAGAGCGACAAACAAATTGACATAAGAGAGACCTCTAGAGTTAGGGACAAAATAGTCCTTTCACGCGGTTAGTTTTGTGC[C/T]
AATAAATAACTTAAGCCCTTCAAAGTATAAAAATAGAGATGGCAATGAAATAGATGGCATTTTATCGAATCTCATCAAATCAAGTGTTAAATCAAACGGC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 88.90% 11.10% 0.04% 0.00% NA
All Indica  2759 93.10% 6.90% 0.00% 0.00% NA
All Japonica  1512 80.00% 19.90% 0.13% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 91.20% 8.80% 0.00% 0.00% NA
Indica III  913 87.10% 12.90% 0.00% 0.00% NA
Indica Intermediate  786 96.10% 3.90% 0.00% 0.00% NA
Temperate Japonica  767 63.50% 36.20% 0.26% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 91.30% 8.70% 0.00% 0.00% NA
VI/Aromatic  96 75.00% 25.00% 0.00% 0.00% NA
Intermediate  90 92.20% 7.80% 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
vg0722260306 G -> A LOC_Os07g37156.1 upstream_gene_variant ; 1853.0bp to feature; MODIFIER silent_mutation Average:73.49; most accessible tissue: Minghui63 panicle, score: 87.951 N N N N
vg0722260306 G -> A LOC_Os07g37150.1 downstream_gene_variant ; 3577.0bp to feature; MODIFIER silent_mutation Average:73.49; most accessible tissue: Minghui63 panicle, score: 87.951 N N N N
vg0722260306 G -> A LOC_Os07g37156-LOC_Os07g37180 intergenic_region ; MODIFIER silent_mutation Average:73.49; most accessible tissue: Minghui63 panicle, score: 87.951 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)
vg0722260306 G A 0.1 0.12 0.04 0.04 0.06 0.05

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0722260306 NA 1.69E-06 mr1229_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
vg0722260306 NA 9.29E-06 mr1305_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
vg0722260306 NA 6.22E-06 mr1555_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
vg0722260306 NA 1.42E-07 mr1585_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
vg0722260306 5.04E-06 5.04E-06 mr1608_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
vg0722260306 2.05E-06 1.07E-09 mr1693_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
vg0722260306 NA 3.66E-08 mr1693_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
vg0722260306 NA 3.69E-06 mr1736_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
vg0722260306 2.27E-07 NA mr1765_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
vg0722260306 8.14E-06 1.04E-08 mr1765_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
vg0722260306 NA 3.22E-06 mr1780_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