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Detailed information for vg1121797475:

Variant ID: vg1121797475 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 21797475
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 313. )

Flanking Sequence (100 bp) in Reference Genome:


TGCTTTAGAATACTCATGGTATTTCTTACAATTCCTTCCTTTTGCTGTTGATGTGCTCAATAATCTAACATATGGACTGCCCTTGTCATGGACTATTGAG[T/A]
ACATGATCAAGTAGAGGCTGTACACCTACATTGCAATAAACAGCAACCTTGTGGACCTGTTCTTTTTTAGAGTGATTAAAATATGTAATTCACGTACTTT

Reverse complement sequence

AAAGTACGTGAATTACATATTTTAATCACTCTAAAAAAGAACAGGTCCACAAGGTTGCTGTTTATTGCAATGTAGGTGTACAGCCTCTACTTGATCATGT[A/T]
CTCAATAGTCCATGACAAGGGCAGTCCATATGTTAGATTATTGAGCACATCAACAGCAAAAGGAAGGAATTGTAAGAAATACCATGAGTATTCTAAAGCA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 99.60% 0.10% 0.21% 0.11% NA
All Indica  2759 99.40% 0.10% 0.33% 0.18% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.00% 0.20% 0.50% 0.34% NA
Indica II  465 99.10% 0.00% 0.22% 0.65% NA
Indica III  913 99.90% 0.00% 0.11% 0.00% NA
Indica Intermediate  786 99.40% 0.10% 0.51% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 1.00% 1.04% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg1121797475 T -> A LOC_Os11g36950.1 intron_variant ; MODIFIER N Average:66.2; most accessible tissue: Zhenshan97 flower, score: 90.356 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)
vg1121797475 T A -0.02 -0.02 -0.02 -0.02 -0.02 -0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1121797475 NA 1.69E-06 mr1038 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
vg1121797475 4.17E-06 NA mr1672 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