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Detailed information for vg0205800449:

Variant ID: vg0205800449 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 5800449
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGCGCGCCGCAGTTGCAGTACCAGTCACCTGGGCGGACATCAGAGCCAGTGCCAAAGCCTCCACCGAAGGAGGAACCACCACGGCCGCCGAAGTTGGCGT[A/G]
GTCACCGCCACCACCGCTGCCGCGATCAGCGGCGCCACGCGGCTCGCCGCAGCGCTGGCATAGGTCCCGGCGGCTGAAGTTGAGGTGCTGGCACGCCCTG

Reverse complement sequence

CAGGGCGTGCCAGCACCTCAACTTCAGCCGCCGGGACCTATGCCAGCGCTGCGGCGAGCCGCGTGGCGCCGCTGATCGCGGCAGCGGTGGTGGCGGTGAC[T/C]
ACGCCAACTTCGGCGGCCGTGGTGGTTCCTCCTTCGGTGGAGGCTTTGGCACTGGCTCTGATGTCCGCCCAGGTGACTGGTACTGCAACTGCGGCGCGCA

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 96.50% 2.00% 1.46% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 89.20% 6.30% 4.50% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 94.40% 0.90% 4.69% 0.00% NA
Tropical Japonica  504 90.70% 8.10% 1.19% 0.00% NA
Japonica Intermediate  241 69.30% 19.90% 10.79% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 0.00% 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
vg0205800449 A -> G LOC_Os02g10920.1 missense_variant ; p.Tyr44His; MODERATE nonsynonymous_codon ; Y44H Average:91.061; most accessible tissue: Minghui63 young leaf, score: 97.06 unknown unknown TOLERATED 0.06
vg0205800449 A -> G LOC_Os02g10920.2 missense_variant ; p.Tyr44His; MODERATE nonsynonymous_codon ; Y44H Average:91.061; most accessible tissue: Minghui63 young leaf, score: 97.06 unknown unknown TOLERATED 0.06
vg0205800449 A -> G LOC_Os02g10920.3 missense_variant ; p.Tyr44His; MODERATE nonsynonymous_codon ; Y44H Average:91.061; most accessible tissue: Minghui63 young leaf, score: 97.06 unknown unknown TOLERATED 0.08
vg0205800449 A -> G LOC_Os02g10920.4 missense_variant ; p.Tyr44His; MODERATE nonsynonymous_codon ; Y44H Average:91.061; most accessible tissue: Minghui63 young leaf, score: 97.06 unknown unknown TOLERATED 0.08
vg0205800449 A -> G LOC_Os02g10920.5 missense_variant ; p.Tyr44His; MODERATE nonsynonymous_codon ; Y44H Average:91.061; most accessible tissue: Minghui63 young leaf, score: 97.06 unknown unknown TOLERATED 0.06
vg0205800449 A -> G LOC_Os02g10920.6 missense_variant ; p.Tyr44His; MODERATE nonsynonymous_codon ; Y44H Average:91.061; most accessible tissue: Minghui63 young leaf, score: 97.06 unknown unknown TOLERATED 0.08

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)
vg0205800449 A G -0.02 -0.02 -0.02 0.0 0.0 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0205800449 NA 5.63E-06 mr1622 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
vg0205800449 2.63E-09 8.36E-08 mr1750_2 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