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Detailed information for vg1022604309:

Variant ID: vg1022604309 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 22604309
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.96, T: 0.04, others allele: 0.00, population size: 97. )

Flanking Sequence (100 bp) in Reference Genome:


GACATATCTATCATAGTACAACGAATCTGAAAAGAGGACTGTCCAGATTCATTATATTAGAATGTGTCTCTAGTATTAGGTTGGTTTTTTATGGGACGGA[G/T]
GGAGTACGTAACATGCCTGCTGCTAGCTAGCTAGCTGTGGGTCTATAAATCGTGAAAACTCAACAGCTATGTAGAGAAGCAACAAATTAACCAAAGAGGG

Reverse complement sequence

CCCTCTTTGGTTAATTTGTTGCTTCTCTACATAGCTGTTGAGTTTTCACGATTTATAGACCCACAGCTAGCTAGCTAGCAGCAGGCATGTTACGTACTCC[C/A]
TCCGTCCCATAAAAAACCAACCTAATACTAGAGACACATTCTAATATAATGAATCTGGACAGTCCTCTTTTCAGATTCGTTGTACTATGATAGATATGTC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 78.40% 20.70% 0.87% 0.00% NA
All Indica  2759 80.60% 19.30% 0.11% 0.00% NA
All Japonica  1512 82.00% 15.50% 2.45% 0.00% NA
Aus  269 29.40% 70.60% 0.00% 0.00% NA
Indica I  595 96.80% 3.20% 0.00% 0.00% NA
Indica II  465 58.90% 41.10% 0.00% 0.00% NA
Indica III  913 83.40% 16.40% 0.22% 0.00% NA
Indica Intermediate  786 77.90% 22.00% 0.13% 0.00% NA
Temperate Japonica  767 72.40% 23.50% 4.17% 0.00% NA
Tropical Japonica  504 97.00% 2.40% 0.60% 0.00% NA
Japonica Intermediate  241 81.30% 17.80% 0.83% 0.00% NA
VI/Aromatic  96 91.70% 8.30% 0.00% 0.00% NA
Intermediate  90 85.60% 13.30% 1.11% 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
vg1022604309 G -> T LOC_Os10g42040.1 upstream_gene_variant ; 3324.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg1022604309 G -> T LOC_Os10g42030.1 downstream_gene_variant ; 2983.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg1022604309 G -> T LOC_Os10g42030-LOC_Os10g42040 intergenic_region ; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 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)
vg1022604309 G T 0.06 0.03 0.01 -0.02 0.02 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1022604309 3.42E-06 7.32E-07 mr1210 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
vg1022604309 6.48E-06 1.87E-06 mr1305 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
vg1022604309 1.73E-07 3.58E-08 mr1585 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
vg1022604309 1.02E-07 8.17E-08 mr1586 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
vg1022604309 NA 7.30E-07 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
vg1022604309 NA 3.86E-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