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Detailed information for vg0309319600:

Variant ID: vg0309319600 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 9319600
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.00, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:


CCTGCATCTTTGGGTGGGGACAGATTGAGCACTTCAGCTAAAGGTTAGGCATCGTGTTCTTGATGAACCAGTGAAGCTAGTGGGCAAAAAAGCCATCGCC[T/C]
ATCTCCCTGAATCACTGAGAGGCTGAGAGCTACGGAATGGCATATCTTAGTCACCAAGTAAAACGTCCACACTGGTAAGCTTCATGTATGATTAAGAAAG

Reverse complement sequence

CTTTCTTAATCATACATGAAGCTTACCAGTGTGGACGTTTTACTTGGTGACTAAGATATGCCATTCCGTAGCTCTCAGCCTCTCAGTGATTCAGGGAGAT[A/G]
GGCGATGGCTTTTTTGCCCACTAGCTTCACTGGTTCATCAAGAACACGATGCCTAACCTTTAGCTGAAGTGCTCAATCTGTCCCCACCCAAAGATGCAGG

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% 0.17% 0.00% NA
All Indica  2759 72.20% 27.70% 0.07% 0.00% NA
All Japonica  1512 22.70% 76.90% 0.40% 0.00% NA
Aus  269 79.60% 20.40% 0.00% 0.00% NA
Indica I  595 93.60% 6.40% 0.00% 0.00% NA
Indica II  465 91.40% 8.60% 0.00% 0.00% NA
Indica III  913 50.70% 49.30% 0.00% 0.00% NA
Indica Intermediate  786 69.70% 30.00% 0.25% 0.00% NA
Temperate Japonica  767 2.90% 97.10% 0.00% 0.00% NA
Tropical Japonica  504 51.40% 47.60% 0.99% 0.00% NA
Japonica Intermediate  241 25.70% 73.90% 0.41% 0.00% NA
VI/Aromatic  96 25.00% 75.00% 0.00% 0.00% NA
Intermediate  90 41.10% 58.90% 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
vg0309319600 T -> C LOC_Os03g16800.1 upstream_gene_variant ; 2888.0bp to feature; MODIFIER silent_mutation Average:86.181; most accessible tissue: Minghui63 flower, score: 94.468 N N N N
vg0309319600 T -> C LOC_Os03g16800.2 upstream_gene_variant ; 3212.0bp to feature; MODIFIER silent_mutation Average:86.181; most accessible tissue: Minghui63 flower, score: 94.468 N N N N
vg0309319600 T -> C LOC_Os03g16800-LOC_Os03g16812 intergenic_region ; MODIFIER silent_mutation Average:86.181; most accessible tissue: Minghui63 flower, score: 94.468 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)
vg0309319600 T C -0.06 -0.07 -0.06 0.01 -0.08 -0.1

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0309319600 NA 8.00E-08 mr1082 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
vg0309319600 NA 5.39E-08 mr1082_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
vg0309319600 7.44E-07 2.52E-08 mr1083_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
vg0309319600 5.57E-06 NA mr1104_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
vg0309319600 NA 7.21E-06 mr1107_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
vg0309319600 NA 8.12E-07 mr1226_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
vg0309319600 2.36E-06 3.72E-08 mr1408_2 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