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Detailed information for vg0609140223:

Variant ID: vg0609140223 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 9140223
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: 259. )

Flanking Sequence (100 bp) in Reference Genome:


CAGCACGATATGAAAGGATGTGCCCAGCCCGTGACAGTCACACTTTAACGGTGCATGGTTTTGTCACCCAAAACAGGGGGACTATGCTACATCGCATTTG[C/T]
AGCCGACAAAATTGATGAGCTGAGATGCAAAGCACGGTCAAGCTAGTTAATTACTTCCTCCATTTCATATTACAAGACTTTATAGCATTGTCCACATTTA

Reverse complement sequence

TAAATGTGGACAATGCTATAAAGTCTTGTAATATGAAATGGAGGAAGTAATTAACTAGCTTGACCGTGCTTTGCATCTCAGCTCATCAATTTTGTCGGCT[G/A]
CAAATGCGATGTAGCATAGTCCCCCTGTTTTGGGTGACAAAACCATGCACCGTTAAAGTGTGACTGTCACGGGCTGGGCACATCCTTTCATATCGTGCTG

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 59.20% 1.20% 7.26% 32.40% NA
All Indica  2759 76.00% 2.00% 6.45% 15.48% NA
All Japonica  1512 41.80% 0.00% 6.28% 51.92% NA
Aus  269 4.10% 0.00% 18.96% 76.95% NA
Indica I  595 78.00% 7.10% 9.41% 5.55% NA
Indica II  465 84.90% 0.00% 4.73% 10.32% NA
Indica III  913 71.10% 0.00% 7.23% 21.69% NA
Indica Intermediate  786 75.10% 1.80% 4.33% 18.83% NA
Temperate Japonica  767 74.70% 0.00% 1.96% 23.34% NA
Tropical Japonica  504 5.60% 0.00% 11.71% 82.74% NA
Japonica Intermediate  241 12.90% 0.00% 8.71% 78.42% NA
VI/Aromatic  96 9.40% 0.00% 14.58% 76.04% NA
Intermediate  90 51.10% 0.00% 5.56% 43.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0609140223 C -> T LOC_Os06g16060.1 upstream_gene_variant ; 2215.0bp to feature; MODIFIER silent_mutation Average:78.26; most accessible tissue: Callus, score: 99.007 N N N N
vg0609140223 C -> T LOC_Os06g16060-LOC_Os06g16070 intergenic_region ; MODIFIER silent_mutation Average:78.26; most accessible tissue: Callus, score: 99.007 N N N N
vg0609140223 C -> DEL N N silent_mutation Average:78.26; most accessible tissue: Callus, score: 99.007 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)
vg0609140223 C T -0.03 -0.01 -0.01 -0.02 0.0 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0609140223 NA 7.79E-07 mr1038 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
vg0609140223 NA 2.10E-08 mr1389 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
vg0609140223 2.07E-06 2.07E-06 mr1521 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
vg0609140223 NA 1.35E-09 mr1038_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
vg0609140223 NA 2.85E-10 mr1389_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