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Detailed information for vg0129154588:

Variant ID: vg0129154588 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 29154588
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.02, others allele: 0.00, population size: 104. )

Flanking Sequence (100 bp) in Reference Genome:


GGCACGATGAATATTTATGCATACACTTGCATGTGAAAAAGATATGCTTGGATTAATTAGGCTAGGTAGACAAGCGGGAAATGTGTAAAAGAGTTTTTTT[G/T]
TGTGTGTGTGTGTGTGTGTGTTGTTTGCGGTGTTGTTGCATCTCTCGAATGTGGTCGATCGAGATGCGCGTGTACGTAGTTTTTTTCAGCAGAAACCAAA

Reverse complement sequence

TTTGGTTTCTGCTGAAAAAAACTACGTACACGCGCATCTCGATCGACCACATTCGAGAGATGCAACAACACCGCAAACAACACACACACACACACACACA[C/A]
AAAAAAACTCTTTTACACATTTCCCGCTTGTCTACCTAGCCTAATTAATCCAAGCATATCTTTTTCACATGCAAGTGTATGCATAAATATTCATCGTGCC

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 68.20% 13.50% 12.17% 6.14% NA
All Indica  2759 66.90% 7.30% 16.46% 9.35% NA
All Japonica  1512 81.50% 13.80% 3.70% 0.99% NA
Aus  269 14.50% 71.40% 13.01% 1.12% NA
Indica I  595 73.80% 2.50% 18.32% 5.38% NA
Indica II  465 67.70% 3.00% 18.92% 10.32% NA
Indica III  913 65.80% 10.60% 12.49% 11.06% NA
Indica Intermediate  786 62.30% 9.70% 18.19% 9.80% NA
Temperate Japonica  767 91.30% 7.60% 1.17% 0.00% NA
Tropical Japonica  504 77.40% 13.50% 6.35% 2.78% NA
Japonica Intermediate  241 58.90% 34.40% 6.22% 0.41% NA
VI/Aromatic  96 43.80% 30.20% 17.71% 8.33% NA
Intermediate  90 71.10% 7.80% 14.44% 6.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0129154588 G -> T LOC_Os01g50750.1 3_prime_UTR_variant ; 248.0bp to feature; MODIFIER silent_mutation Average:95.044; most accessible tissue: Zhenshan97 flower, score: 97.294 N N N N
vg0129154588 G -> T LOC_Os01g50760.1 upstream_gene_variant ; 3675.0bp to feature; MODIFIER silent_mutation Average:95.044; most accessible tissue: Zhenshan97 flower, score: 97.294 N N N N
vg0129154588 G -> T LOC_Os01g50740.1 downstream_gene_variant ; 4975.0bp to feature; MODIFIER silent_mutation Average:95.044; most accessible tissue: Zhenshan97 flower, score: 97.294 N N N N
vg0129154588 G -> DEL N N silent_mutation Average:95.044; most accessible tissue: Zhenshan97 flower, score: 97.294 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)
vg0129154588 G T 0.02 0.0 0.0 -0.01 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0129154588 NA 4.61E-20 Plant_height All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0129154588 NA 8.37E-06 mr1070 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
vg0129154588 NA 5.93E-13 mr1180 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
vg0129154588 NA 3.25E-09 mr1839 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
vg0129154588 4.19E-06 2.62E-06 mr1890 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
vg0129154588 NA 1.33E-06 mr1909 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
vg0129154588 NA 2.19E-06 mr1268_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
vg0129154588 NA 8.84E-07 mr1695_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
vg0129154588 NA 3.33E-15 mr1794_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
vg0129154588 NA 1.48E-06 mr1815_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