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Detailed information for vg0137602014:

Variant ID: vg0137602014 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 37602014
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 304. )

Flanking Sequence (100 bp) in Reference Genome:


TTTATAAAGGAGGCTTGAACCAGATGTGGACGGGGAAGAGGAACAACGGAATCATACCCCATTTACACAAATGCTATTGTGACAGGCGGTTGATGCAGGG[C/T]
GTTCATTGCATAAAATACTTCAGACTGATCCCTAACAATATTGTACACAATTTTATTAGCCAAATCCGGTTGAACACACACAATTGGCGAAGAACAAGAA

Reverse complement sequence

TTCTTGTTCTTCGCCAATTGTGTGTGTTCAACCGGATTTGGCTAATAAAATTGTGTACAATATTGTTAGGGATCAGTCTGAAGTATTTTATGCAATGAAC[G/A]
CCCTGCATCAACCGCCTGTCACAATAGCATTTGTGTAAATGGGGTATGATTCCGTTGTTCCTCTTCCCCGTCCACATCTGGTTCAAGCCTCCTTTATAAA

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 93.10% 5.50% 1.31% 0.00% NA
All Indica  2759 88.40% 9.40% 2.21% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 65.00% 27.40% 7.56% 0.00% NA
Indica II  465 97.20% 2.40% 0.43% 0.00% NA
Indica III  913 97.00% 2.70% 0.22% 0.00% NA
Indica Intermediate  786 90.70% 7.80% 1.53% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 0.00% 1.11% 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
vg0137602014 C -> T LOC_Os01g64800-LOC_Os01g64810 intergenic_region ; MODIFIER silent_mutation Average:78.66; most accessible tissue: Zhenshan97 young leaf, score: 93.68 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)
vg0137602014 C T -0.03 -0.06 -0.06 -0.03 -0.05 -0.06

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0137602014 1.86E-08 NA mr1517 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
vg0137602014 8.72E-13 1.75E-13 mr1517 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
vg0137602014 NA 8.10E-06 mr1518 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
vg0137602014 5.34E-06 NA mr1538 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
vg0137602014 9.91E-09 4.57E-08 mr1538 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
vg0137602014 1.19E-06 1.73E-07 mr1676 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
vg0137602014 4.09E-06 8.23E-07 mr1517_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