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Detailed information for vg0137838376:

Variant ID: vg0137838376 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 37838376
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.98, G: 0.01, others allele: 0.00, population size: 126. )

Flanking Sequence (100 bp) in Reference Genome:


TTGTTCGGTTTATAACATACTAAGTCGTGCATAAAGTACTATTTATGTTTTACTATCTCTTAACAACAAAACTATTAATTATAAAAAATTTTCAAATAAG[A/G]
CGGATGATTAAAGTTGGACACGAAAACTCATAGTTGCACTTAAAATGGGAAGGAGGGAGTATAATATTTGGTTCTTCTTTATTTAAGTAGATCATCAATC

Reverse complement sequence

GATTGATGATCTACTTAAATAAAGAAGAACCAAATATTATACTCCCTCCTTCCCATTTTAAGTGCAACTATGAGTTTTCGTGTCCAACTTTAATCATCCG[T/C]
CTTATTTGAAAATTTTTTATAATTAATAGTTTTGTTGTTAAGAGATAGTAAAACATAAATAGTACTTTATGCACGACTTAGTATGTTATAAACCGAACAA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 52.70% 46.90% 0.25% 0.19% NA
All Indica  2759 31.10% 68.20% 0.36% 0.33% NA
All Japonica  1512 97.70% 2.20% 0.07% 0.00% NA
Aus  269 0.40% 99.30% 0.37% 0.00% NA
Indica I  595 36.60% 62.50% 0.34% 0.50% NA
Indica II  465 14.80% 84.30% 0.43% 0.43% NA
Indica III  913 39.50% 60.10% 0.11% 0.22% NA
Indica Intermediate  786 26.60% 72.50% 0.64% 0.25% NA
Temperate Japonica  767 97.90% 2.10% 0.00% 0.00% NA
Tropical Japonica  504 97.80% 2.20% 0.00% 0.00% NA
Japonica Intermediate  241 96.70% 2.90% 0.41% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 67.80% 32.20% 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
vg0137838376 A -> G LOC_Os01g65200.3 downstream_gene_variant ; 1450.0bp to feature; MODIFIER silent_mutation Average:73.189; most accessible tissue: Minghui63 flower, score: 94.309 N N N N
vg0137838376 A -> G LOC_Os01g65200.1 downstream_gene_variant ; 1450.0bp to feature; MODIFIER silent_mutation Average:73.189; most accessible tissue: Minghui63 flower, score: 94.309 N N N N
vg0137838376 A -> G LOC_Os01g65200.2 downstream_gene_variant ; 1450.0bp to feature; MODIFIER silent_mutation Average:73.189; most accessible tissue: Minghui63 flower, score: 94.309 N N N N
vg0137838376 A -> G LOC_Os01g65210.1 intron_variant ; MODIFIER silent_mutation Average:73.189; most accessible tissue: Minghui63 flower, score: 94.309 N N N N
vg0137838376 A -> DEL N N silent_mutation Average:73.189; most accessible tissue: Minghui63 flower, score: 94.309 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)
vg0137838376 A G -0.06 -0.04 -0.03 -0.02 -0.03 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0137838376 NA 3.75E-13 mr1170 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
vg0137838376 1.70E-08 1.43E-34 mr1375 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
vg0137838376 9.28E-07 5.16E-09 mr1375 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
vg0137838376 3.58E-21 4.75E-86 mr1517 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
vg0137838376 3.55E-17 9.76E-21 mr1517 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
vg0137838376 4.69E-18 4.35E-69 mr1538 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
vg0137838376 5.28E-12 8.86E-15 mr1538 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
vg0137838376 1.27E-24 NA mr1517_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
vg0137838376 1.57E-21 2.51E-23 mr1517_2 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
vg0137838376 3.64E-20 NA mr1538_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
vg0137838376 1.01E-14 8.90E-22 mr1538_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