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Detailed information for vg0903407929:

Variant ID: vg0903407929 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 3407929
Reference Allele: TAlternative Allele: A
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.97, A: 0.03, others allele: 0.00, population size: 116. )

Flanking Sequence (100 bp) in Reference Genome:


ATAGTGCGGTTGGGTTGGGTTGGGTTGGGTTGGGGATTTTGGATTGCTGCGATAGCGGGGTGACTTTCGACGTCATGTGCGGCGTTTTATAGAACCAAAG[T/A]
GTAAGAAAAAAATGGGAAAGTATGTAGTGGAAACCTATACGATTGGATTGCCCGAAAAAAATGATGCGATATGCGGTGCGCTCTGACCCCCGACCCGAGT

Reverse complement sequence

ACTCGGGTCGGGGGTCAGAGCGCACCGCATATCGCATCATTTTTTTCGGGCAATCCAATCGTATAGGTTTCCACTACATACTTTCCCATTTTTTTCTTAC[A/T]
CTTTGGTTCTATAAAACGCCGCACATGACGTCGAAAGTCACCCCGCTATCGCAGCAATCCAAAATCCCCAACCCAACCCAACCCAACCCAACCGCACTAT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 54.60% 45.30% 0.04% 0.00% NA
All Indica  2759 89.90% 10.10% 0.04% 0.00% NA
All Japonica  1512 0.90% 99.10% 0.07% 0.00% NA
Aus  269 17.80% 82.20% 0.00% 0.00% NA
Indica I  595 94.60% 5.40% 0.00% 0.00% NA
Indica II  465 85.20% 14.80% 0.00% 0.00% NA
Indica III  913 93.40% 6.60% 0.00% 0.00% NA
Indica Intermediate  786 84.90% 15.00% 0.13% 0.00% NA
Temperate Japonica  767 0.80% 99.20% 0.00% 0.00% NA
Tropical Japonica  504 1.00% 99.00% 0.00% 0.00% NA
Japonica Intermediate  241 0.80% 98.80% 0.41% 0.00% NA
VI/Aromatic  96 4.20% 95.80% 0.00% 0.00% NA
Intermediate  90 42.20% 57.80% 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
vg0903407929 T -> A LOC_Os09g07020.1 synonymous_variant ; p.Thr41Thr; LOW synonymous_codon Average:94.831; most accessible tissue: Zhenshan97 root, score: 97.059 N N N N
vg0903407929 T -> A LOC_Os09g07020.2 synonymous_variant ; p.Thr41Thr; LOW synonymous_codon Average:94.831; most accessible tissue: Zhenshan97 root, score: 97.059 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)
vg0903407929 T A 0.02 -0.01 -0.01 -0.01 0.0 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0903407929 NA 5.21E-38 mr1208_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
vg0903407929 NA 3.20E-07 mr1446_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
vg0903407929 NA 2.01E-08 mr1660_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