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Detailed information for vg1022149399:

Variant ID: vg1022149399 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 22149399
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: 236. )

Flanking Sequence (100 bp) in Reference Genome:


AGATTTATACCGACATTGTTAAAAGGATAATTAGCTGTAAATACGAGCATCCATATAACTGATCTCATGATTTCGTTGGAACACATGTTTTTGTACGTAC[C/T]
CCTCCGTCAAAAAAATTTAATCCTAGCTATGAACCTGGACATATACGTATCCAGGTTCGTAGCCAGTTTTTGGACATAGTAGTAAGCAATAGGAATCGGT

Reverse complement sequence

ACCGATTCCTATTGCTTACTACTATGTCCAAAAACTGGCTACGAACCTGGATACGTATATGTCCAGGTTCATAGCTAGGATTAAATTTTTTTGACGGAGG[G/A]
GTACGTACAAAAACATGTGTTCCAACGAAATCATGAGATCAGTTATATGGATGCTCGTATTTACAGCTAATTATCCTTTTAACAATGTCGGTATAAATCT

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 51.30% 48.30% 0.19% 0.17% NA
All Indica  2759 18.90% 80.70% 0.18% 0.25% NA
All Japonica  1512 99.50% 0.30% 0.07% 0.07% NA
Aus  269 90.00% 10.00% 0.00% 0.00% NA
Indica I  595 15.30% 84.40% 0.17% 0.17% NA
Indica II  465 16.60% 83.40% 0.00% 0.00% NA
Indica III  913 24.20% 75.50% 0.22% 0.11% NA
Indica Intermediate  786 16.80% 82.30% 0.25% 0.64% NA
Temperate Japonica  767 99.50% 0.30% 0.13% 0.13% NA
Tropical Japonica  504 99.40% 0.60% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 0.00% 1.04% 0.00% NA
Intermediate  90 67.80% 30.00% 2.22% 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
vg1022149399 C -> T LOC_Os10g41224.1 upstream_gene_variant ; 850.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg1022149399 C -> T LOC_Os10g41230.1 upstream_gene_variant ; 3232.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg1022149399 C -> T LOC_Os10g41220-LOC_Os10g41224 intergenic_region ; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg1022149399 C -> DEL N N silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 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)
vg1022149399 C T 0.01 0.01 0.01 -0.01 0.01 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1022149399 NA 7.36E-13 mr1189_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
vg1022149399 NA 1.85E-07 mr1527_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
vg1022149399 NA 3.01E-07 mr1629_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
vg1022149399 NA 4.66E-11 mr1734_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
vg1022149399 NA 7.80E-09 mr1751_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
vg1022149399 NA 3.50E-09 mr1834_2 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