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Detailed information for vg1202975555:

Variant ID: vg1202975555 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 2975555
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.01, others allele: 0.00, population size: 281. )

Flanking Sequence (100 bp) in Reference Genome:


CCCAAACAGACCGCTCTATACACATCTGCTAGCCTCATATGTTGTTTGTTTGAGGATGGTGACTCTACTCCAAATGCATGTTGACAACATGTATTTCGTA[T/C]
ATGCATCAAAATCAATCTGATATTTTGTCCGTTACATCAAAACTGCATATGCACTTCATGCAATTTTAGTTTTACGCACACCAACAATATTAGTTTTAAA

Reverse complement sequence

TTTAAAACTAATATTGTTGGTGTGCGTAAAACTAAAATTGCATGAAGTGCATATGCAGTTTTGATGTAACGGACAAAATATCAGATTGATTTTGATGCAT[A/G]
TACGAAATACATGTTGTCAACATGCATTTGGAGTAGAGTCACCATCCTCAAACAAACAACATATGAGGCTAGCAGATGTGTATAGAGCGGTCTGTTTGGG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 91.60% 6.90% 1.46% 0.00% NA
All Indica  2759 98.80% 0.40% 0.76% 0.00% NA
All Japonica  1512 77.10% 20.20% 2.78% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 98.50% 0.00% 1.51% 0.00% NA
Indica II  465 99.10% 0.60% 0.22% 0.00% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 97.70% 0.90% 1.40% 0.00% NA
Temperate Japonica  767 95.80% 2.60% 1.56% 0.00% NA
Tropical Japonica  504 50.80% 44.80% 4.37% 0.00% NA
Japonica Intermediate  241 72.20% 24.50% 3.32% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 83.30% 10.00% 6.67% 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
vg1202975555 T -> C LOC_Os12g06250.1 downstream_gene_variant ; 1395.0bp to feature; MODIFIER silent_mutation Average:83.222; most accessible tissue: Callus, score: 91.411 N N N N
vg1202975555 T -> C LOC_Os12g06260.1 downstream_gene_variant ; 3922.0bp to feature; MODIFIER silent_mutation Average:83.222; most accessible tissue: Callus, score: 91.411 N N N N
vg1202975555 T -> C LOC_Os12g06250.2 downstream_gene_variant ; 1395.0bp to feature; MODIFIER silent_mutation Average:83.222; most accessible tissue: Callus, score: 91.411 N N N N
vg1202975555 T -> C LOC_Os12g06250-LOC_Os12g06260 intergenic_region ; MODIFIER silent_mutation Average:83.222; most accessible tissue: Callus, score: 91.411 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)
vg1202975555 T C 0.01 0.01 0.01 0.01 0.02 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1202975555 6.48E-08 NA Grain_thickness All YES Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg1202975555 NA 3.36E-14 Grain_thickness Jap_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg1202975555 NA 9.91E-07 mr1248 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
vg1202975555 8.27E-06 NA mr1226_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
vg1202975555 NA 8.23E-06 mr1425_2 Jap_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
vg1202975555 NA 5.67E-07 mr1819_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