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Detailed information for vg1128937803:

Variant ID: vg1128937803 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 28937803
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.66, C: 0.34, others allele: 0.00, population size: 85. )

Flanking Sequence (100 bp) in Reference Genome:


TATGTGCAAAAATACTAATAATGTATTAGTATATGACAAGTGTAATTTCACCACATATCACATACTTCGAGGTATTAAAATTTGTAGTGTAAAATTTTAG[T/C]
ATGTACTATACTTTAAAAATTCTCATACGATTAATTTAAATAATACTAGTTAATTTGGGTGCAGTAGTGACAAATTAAACGTTCCTCTTTGTTAAGGGTA

Reverse complement sequence

TACCCTTAACAAAGAGGAACGTTTAATTTGTCACTACTGCACCCAAATTAACTAGTATTATTTAAATTAATCGTATGAGAATTTTTAAAGTATAGTACAT[A/G]
CTAAAATTTTACACTACAAATTTTAATACCTCGAAGTATGTGATATGTGGTGAAATTACACTTGTCATATACTAATACATTATTAGTATTTTTGCACATA

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 55.20% 44.60% 0.11% 0.00% NA
All Indica  2759 83.40% 16.50% 0.11% 0.00% NA
All Japonica  1512 4.80% 95.00% 0.13% 0.00% NA
Aus  269 71.00% 29.00% 0.00% 0.00% NA
Indica I  595 91.90% 7.90% 0.17% 0.00% NA
Indica II  465 85.60% 14.40% 0.00% 0.00% NA
Indica III  913 77.80% 22.10% 0.11% 0.00% NA
Indica Intermediate  786 82.10% 17.80% 0.13% 0.00% NA
Temperate Japonica  767 6.00% 93.70% 0.26% 0.00% NA
Tropical Japonica  504 4.20% 95.80% 0.00% 0.00% NA
Japonica Intermediate  241 2.50% 97.50% 0.00% 0.00% NA
VI/Aromatic  96 7.30% 92.70% 0.00% 0.00% NA
Intermediate  90 44.40% 55.60% 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
vg1128937803 T -> C LOC_Os11g47970.1 upstream_gene_variant ; 1463.0bp to feature; MODIFIER silent_mutation Average:73.058; most accessible tissue: Minghui63 flag leaf, score: 96.613 N N N N
vg1128937803 T -> C LOC_Os11g47960.1 downstream_gene_variant ; 4825.0bp to feature; MODIFIER silent_mutation Average:73.058; most accessible tissue: Minghui63 flag leaf, score: 96.613 N N N N
vg1128937803 T -> C LOC_Os11g47980.1 downstream_gene_variant ; 225.0bp to feature; MODIFIER silent_mutation Average:73.058; most accessible tissue: Minghui63 flag leaf, score: 96.613 N N N N
vg1128937803 T -> C LOC_Os11g47990.1 downstream_gene_variant ; 2889.0bp to feature; MODIFIER silent_mutation Average:73.058; most accessible tissue: Minghui63 flag leaf, score: 96.613 N N N N
vg1128937803 T -> C LOC_Os11g47970-LOC_Os11g47980 intergenic_region ; MODIFIER silent_mutation Average:73.058; most accessible tissue: Minghui63 flag leaf, score: 96.613 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)
vg1128937803 T C 0.01 0.0 0.0 -0.01 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1128937803 9.07E-07 1.66E-08 mr1019_2 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