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Detailed information for vg1124940229:

Variant ID: vg1124940229 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 24940229
Reference Allele: AAlternative Allele: T
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.57, A: 0.43, others allele: 0.00, population size: 42. )

Flanking Sequence (100 bp) in Reference Genome:


ACTGTTCGGGTACTCACGCCCGAAGAATTACTATCGAAGCCACACAAATGGTATATTTCTTAGATAATGGAATAGAGCATCCCGGTCTTTCCTGAAAAAA[A/T]
TTTGAAAATATATCTCTTTTTTTCATAATTTGCGTTTATATACCTGCATGGCGGAGATTTGCACAAATATACCTAATCCGCGGGTTGGAGATGCGGGAGC

Reverse complement sequence

GCTCCCGCATCTCCAACCCGCGGATTAGGTATATTTGTGCAAATCTCCGCCATGCAGGTATATAAACGCAAATTATGAAAAAAAGAGATATATTTTCAAA[T/A]
TTTTTTCAGGAAAGACCGGGATGCTCTATTCCATTATCTAAGAAATATACCATTTGTGTGGCTTCGATAGTAATTCTTCGGGCGTGAGTACCCGAACAGT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 67.90% 32.00% 0.08% 0.00% NA
All Indica  2759 93.60% 6.40% 0.04% 0.00% NA
All Japonica  1512 22.80% 77.10% 0.13% 0.00% NA
Aus  269 69.50% 30.50% 0.00% 0.00% NA
Indica I  595 99.50% 0.50% 0.00% 0.00% NA
Indica II  465 85.40% 14.40% 0.22% 0.00% NA
Indica III  913 98.00% 2.00% 0.00% 0.00% NA
Indica Intermediate  786 88.80% 11.20% 0.00% 0.00% NA
Temperate Japonica  767 6.40% 93.50% 0.13% 0.00% NA
Tropical Japonica  504 39.10% 60.90% 0.00% 0.00% NA
Japonica Intermediate  241 40.70% 58.90% 0.41% 0.00% NA
VI/Aromatic  96 42.70% 57.30% 0.00% 0.00% NA
Intermediate  90 60.00% 38.90% 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
vg1124940229 A -> T LOC_Os11g41570.1 upstream_gene_variant ; 315.0bp to feature; MODIFIER silent_mutation Average:91.664; most accessible tissue: Callus, score: 97.273 N N N N
vg1124940229 A -> T LOC_Os11g41580.1 downstream_gene_variant ; 1237.0bp to feature; MODIFIER silent_mutation Average:91.664; most accessible tissue: Callus, score: 97.273 N N N N
vg1124940229 A -> T LOC_Os11g41570-LOC_Os11g41580 intergenic_region ; MODIFIER silent_mutation Average:91.664; most accessible tissue: Callus, score: 97.273 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)
vg1124940229 A T 0.01 0.01 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
vg1124940229 4.31E-09 9.67E-28 mr1238 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
vg1124940229 6.02E-08 2.74E-09 mr1238 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
vg1124940229 2.77E-07 1.44E-28 mr1309 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
vg1124940229 1.40E-06 1.04E-07 mr1309 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
vg1124940229 9.34E-06 1.82E-17 mr1484 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
vg1124940229 2.55E-06 1.83E-06 mr1484 Ind_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
vg1124940229 3.37E-06 1.25E-25 mr1841 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
vg1124940229 NA 1.14E-06 mr1841 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
vg1124940229 NA 1.30E-10 mr1945 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
vg1124940229 2.13E-08 2.02E-29 mr1238_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
vg1124940229 1.66E-06 NA mr1238_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
vg1124940229 2.30E-08 1.74E-27 mr1484_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
vg1124940229 1.07E-06 6.04E-06 mr1484_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
vg1124940229 4.48E-08 2.63E-33 mr1841_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
vg1124940229 3.09E-06 NA mr1841_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
vg1124940229 6.68E-08 6.30E-21 mr1900_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
vg1124940229 4.78E-06 NA mr1900_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
vg1124940229 3.18E-07 1.41E-20 mr1945_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