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Detailed information for vg0128084573:

Variant ID: vg0128084573 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 28084573
Reference Allele: CAlternative Allele: A
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.73, A: 0.25, T: 0.02, others allele: 0.00, population size: 200. )

Flanking Sequence (100 bp) in Reference Genome:


TATGAAAAGCATGCTAATAAAAAGCGGTAAAATCTGTATATCAGAAAAGAACGGGTCTTTATCTAATTGTGATTTGTCGTTTCAGTCAATTTTCACTTTC[C/A]
GGTGACTTGTACGAGACCGCTGTGCGGTCGCAACTCGCAAGACTATCCAGAACTTTGTACCGAGACCAAACAAGTGGAATGGAAAATCCTGCAGCACCAC

Reverse complement sequence

GTGGTGCTGCAGGATTTTCCATTCCACTTGTTTGGTCTCGGTACAAAGTTCTGGATAGTCTTGCGAGTTGCGACCGCACAGCGGTCTCGTACAAGTCACC[G/T]
GAAAGTGAAAATTGACTGAAACGACAAATCACAATTAGATAAAGACCCGTTCTTTTCTGATATACAGATTTTACCGCTTTTTATTAGCATGCTTTTCATA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 70.00% 29.90% 0.04% 0.00% NA
All Indica  2759 99.10% 0.90% 0.00% 0.00% NA
All Japonica  1512 11.70% 88.20% 0.07% 0.00% NA
Aus  269 96.30% 3.70% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 96.80% 3.20% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 98.70% 1.30% 0.00% 0.00% NA
Temperate Japonica  767 0.50% 99.50% 0.00% 0.00% NA
Tropical Japonica  504 31.50% 68.30% 0.20% 0.00% NA
Japonica Intermediate  241 5.80% 94.20% 0.00% 0.00% NA
VI/Aromatic  96 91.70% 8.30% 0.00% 0.00% NA
Intermediate  90 57.80% 41.10% 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
vg0128084573 C -> A LOC_Os01g48930.1 downstream_gene_variant ; 1185.0bp to feature; MODIFIER silent_mutation Average:89.62; most accessible tissue: Zhenshan97 young leaf, score: 98.642 N N N N
vg0128084573 C -> A LOC_Os01g48950.1 downstream_gene_variant ; 3826.0bp to feature; MODIFIER silent_mutation Average:89.62; most accessible tissue: Zhenshan97 young leaf, score: 98.642 N N N N
vg0128084573 C -> A LOC_Os01g48930.2 downstream_gene_variant ; 1185.0bp to feature; MODIFIER silent_mutation Average:89.62; most accessible tissue: Zhenshan97 young leaf, score: 98.642 N N N N
vg0128084573 C -> A LOC_Os01g48940.1 intron_variant ; MODIFIER silent_mutation Average:89.62; most accessible tissue: Zhenshan97 young leaf, score: 98.642 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)
vg0128084573 C A 0.02 0.02 -0.01 0.0 0.03 0.05

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0128084573 NA 7.57E-10 mr1175 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
vg0128084573 NA 6.00E-15 mr1276 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
vg0128084573 NA 8.63E-36 mr1350 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
vg0128084573 NA 8.57E-07 mr1532 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
vg0128084573 7.49E-08 NA mr1871 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
vg0128084573 NA 1.62E-08 mr1986 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
vg0128084573 NA 2.25E-39 mr1243_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
vg0128084573 NA 6.36E-15 mr1277_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
vg0128084573 NA 9.24E-24 mr1350_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
vg0128084573 NA 1.82E-29 mr1423_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
vg0128084573 NA 5.55E-58 mr1599_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
vg0128084573 NA 1.08E-57 mr1695_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
vg0128084573 NA 1.62E-16 mr1730_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
vg0128084573 NA 4.88E-53 mr1991_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