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Detailed information for vg0224660997:

Variant ID: vg0224660997 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 24660997
Reference Allele: CAlternative Allele: A,T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TATATACTCTCTCCATTCAACAAAATAAATAAATTCTAGGCCTGGTTTAGTTTTCAACTTTTTCTTTAAACTTCTAACTTTTATATCACATTAAAACTTT[C/A,T]
CTACACACATAAACTTTCAATTTTTCCGTCACATAGTTTCAATTTTAATCAAACTTCCAATTTTAGCGTGAACTAAACACACCCCTAGACAAATACTCCA

Reverse complement sequence

TGGAGTATTTGTCTAGGGGTGTGTTTAGTTCACGCTAAAATTGGAAGTTTGATTAAAATTGAAACTATGTGACGGAAAAATTGAAAGTTTATGTGTGTAG[G/T,A]
AAAGTTTTAATGTGATATAAAAGTTAGAAGTTTAAAGAAAAAGTTGAAAACTAAACCAGGCCTAGAATTTATTTATTTTGTTGAATGGAGAGAGTATATA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.00% 5.40% 0.08% 0.19% A: 0.32%
All Indica  2759 90.60% 8.80% 0.04% 0.00% A: 0.51%
All Japonica  1512 99.30% 0.00% 0.00% 0.60% A: 0.07%
Aus  269 96.70% 2.20% 1.12% 0.00% NA
Indica I  595 96.50% 3.50% 0.00% 0.00% NA
Indica II  465 90.10% 9.70% 0.00% 0.00% A: 0.22%
Indica III  913 85.30% 13.40% 0.11% 0.00% A: 1.20%
Indica Intermediate  786 92.70% 7.00% 0.00% 0.00% A: 0.25%
Temperate Japonica  767 99.90% 0.00% 0.00% 0.00% A: 0.13%
Tropical Japonica  504 99.40% 0.00% 0.00% 0.60% NA
Japonica Intermediate  241 97.50% 0.00% 0.00% 2.49% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 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
vg0224660997 C -> A LOC_Os02g40664-LOC_Os02g40680 intergenic_region ; MODIFIER silent_mutation Average:69.499; most accessible tissue: Minghui63 panicle, score: 87.238 N N N N
vg0224660997 C -> T LOC_Os02g40664-LOC_Os02g40680 intergenic_region ; MODIFIER silent_mutation Average:69.499; most accessible tissue: Minghui63 panicle, score: 87.238 N N N N
vg0224660997 C -> DEL N N silent_mutation Average:69.499; most accessible tissue: Minghui63 panicle, score: 87.238 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)
vg0224660997 C A -0.02 -0.01 -0.01 -0.01 -0.01 -0.01
vg0224660997 C T 0.03 0.04 0.04 0.0 0.02 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0224660997 4.38E-06 NA mr1795 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
vg0224660997 4.35E-06 3.28E-07 mr1795 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
vg0224660997 NA 1.25E-08 mr1769_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