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Detailed information for vg1100371980:

Variant ID: vg1100371980 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 371980
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 119. )

Flanking Sequence (100 bp) in Reference Genome:


GTAAAATGCAAAGGAAAAAGTACACCGAAGGTCCCTCAACTTGTAATCGAGTTACAAAATCGTCCCCCAACCACAAAACTAGATATATGACATCCCTCAT[C/T]
TTACAAAACCGTTCATTTTAAGTCCCTCGGTGGTTTTGACCCCGGTTTTGTCCGATGTGGCAGTTGAGTCAGCATGAGACCCACGTAGGCCCCACATGTC

Reverse complement sequence

GACATGTGGGGCCTACGTGGGTCTCATGCTGACTCAACTGCCACATCGGACAAAACCGGGGTCAAAACCACCGAGGGACTTAAAATGAACGGTTTTGTAA[G/A]
ATGAGGGATGTCATATATCTAGTTTTGTGGTTGGGGGACGATTTTGTAACTCGATTACAAGTTGAGGGACCTTCGGTGTACTTTTTCCTTTGCATTTTAC

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 95.00% 2.90% 1.59% 0.51% NA
All Indica  2759 98.10% 1.30% 0.47% 0.14% NA
All Japonica  1512 88.30% 6.30% 4.03% 1.32% NA
Aus  269 99.60% 0.00% 0.37% 0.00% NA
Indica I  595 99.80% 0.00% 0.17% 0.00% NA
Indica II  465 90.50% 6.70% 2.15% 0.65% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.10% 0.50% 0.25% 0.13% NA
Temperate Japonica  767 79.80% 10.70% 7.56% 1.96% NA
Tropical Japonica  504 99.60% 0.20% 0.20% 0.00% NA
Japonica Intermediate  241 91.70% 5.40% 0.83% 2.07% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 95.60% 4.40% 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
vg1100371980 C -> T LOC_Os11g01660.1 downstream_gene_variant ; 1179.0bp to feature; MODIFIER silent_mutation Average:86.364; most accessible tissue: Zhenshan97 panicle, score: 97.094 N N N N
vg1100371980 C -> T LOC_Os11g01670.1 downstream_gene_variant ; 99.0bp to feature; MODIFIER silent_mutation Average:86.364; most accessible tissue: Zhenshan97 panicle, score: 97.094 N N N N
vg1100371980 C -> T LOC_Os11g01690.1 downstream_gene_variant ; 4067.0bp to feature; MODIFIER silent_mutation Average:86.364; most accessible tissue: Zhenshan97 panicle, score: 97.094 N N N N
vg1100371980 C -> T LOC_Os11g01660-LOC_Os11g01670 intergenic_region ; MODIFIER silent_mutation Average:86.364; most accessible tissue: Zhenshan97 panicle, score: 97.094 N N N N
vg1100371980 C -> DEL N N silent_mutation Average:86.364; most accessible tissue: Zhenshan97 panicle, score: 97.094 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)
vg1100371980 C T 0.03 0.01 0.03 0.02 0.04 0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1100371980 9.19E-07 NA mr1613 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