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Detailed information for vg0604859044:

Variant ID: vg0604859044 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 4859044
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:


TATATCAACATATTTTTGCTCATATTTAAAAAAGTAAAAAGAATTCCTCAAAAATTTAATATTTGGGTTTCCTAAAAAAAATTAAATTTTTGGAAGATGA[T/C]
GAGCAGCTACTTCAAGCAGGCTAATTGGGAAAAGAAGAGGGCTTGCGCTTGCCAACTCCTAATTGCCAACCAAACTGGGCTATTCTAGATCTATGCTTTA

Reverse complement sequence

TAAAGCATAGATCTAGAATAGCCCAGTTTGGTTGGCAATTAGGAGTTGGCAAGCGCAAGCCCTCTTCTTTTCCCAATTAGCCTGCTTGAAGTAGCTGCTC[A/G]
TCATCTTCCAAAAATTTAATTTTTTTTAGGAAACCCAAATATTAAATTTTTGAGGAATTCTTTTTACTTTTTTAAATATGAGCAAAAATATGTTGATATA

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 84.60% 15.30% 0.04% 0.00% NA
All Indica  2759 76.70% 23.30% 0.07% 0.00% NA
All Japonica  1512 95.40% 4.60% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 59.80% 39.80% 0.34% 0.00% NA
Indica II  465 93.80% 6.20% 0.00% 0.00% NA
Indica III  913 74.90% 25.10% 0.00% 0.00% NA
Indica Intermediate  786 81.30% 18.70% 0.00% 0.00% NA
Temperate Japonica  767 98.30% 1.70% 0.00% 0.00% NA
Tropical Japonica  504 91.30% 8.70% 0.00% 0.00% NA
Japonica Intermediate  241 95.00% 5.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 86.70% 13.30% 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
vg0604859044 T -> C LOC_Os06g09540.1 upstream_gene_variant ; 4285.0bp to feature; MODIFIER silent_mutation Average:70.16; most accessible tissue: Zhenshan97 flower, score: 95.855 N N N N
vg0604859044 T -> C LOC_Os06g09550.1 downstream_gene_variant ; 3936.0bp to feature; MODIFIER silent_mutation Average:70.16; most accessible tissue: Zhenshan97 flower, score: 95.855 N N N N
vg0604859044 T -> C LOC_Os06g09540-LOC_Os06g09550 intergenic_region ; MODIFIER silent_mutation Average:70.16; most accessible tissue: Zhenshan97 flower, score: 95.855 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)
vg0604859044 T C 0.06 -0.01 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
vg0604859044 5.02E-09 4.67E-18 mr1201 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
vg0604859044 1.22E-06 2.17E-18 mr1201 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
vg0604859044 8.82E-08 1.76E-13 mr1219 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
vg0604859044 NA 6.17E-15 mr1219 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
vg0604859044 NA 4.02E-06 mr1236 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
vg0604859044 2.51E-08 7.91E-19 mr1274 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
vg0604859044 1.30E-06 2.67E-16 mr1274 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
vg0604859044 5.08E-08 5.33E-16 mr1201_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
vg0604859044 5.68E-07 9.62E-16 mr1201_2 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
vg0604859044 7.89E-08 1.20E-12 mr1219_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
vg0604859044 2.45E-06 6.10E-14 mr1219_2 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
vg0604859044 NA 1.42E-06 mr1236_2 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
vg0604859044 4.91E-08 6.43E-18 mr1274_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
vg0604859044 3.11E-06 4.71E-17 mr1274_2 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
vg0604859044 NA 3.96E-06 mr1611_2 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