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Detailed information for vg0910836349:

Variant ID: vg0910836349 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 10836349
Reference Allele: TAlternative Allele: A
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGGATCACCGGGCTCACCTGACAACGGTGAGGCCGCGCTCCGATCTGGCGGCGGCGGCGGCAGTGGAGGTCGCCAAATCTAGAGGCGCACGCGCGGCGAG[T/A]
GAGGGAGGAGAGGAGAGAGGCGGGGTTAGGGGCGTGCATGCAGGAGTACTAGTAGAAGCCATAGGGGAAGGGGAAGCGAGGCAGTTGGGGTATTTTATAT

Reverse complement sequence

ATATAAAATACCCCAACTGCCTCGCTTCCCCTTCCCCTATGGCTTCTACTAGTACTCCTGCATGCACGCCCCTAACCCCGCCTCTCTCCTCTCCTCCCTC[A/T]
CTCGCCGCGCGTGCGCCTCTAGATTTGGCGACCTCCACTGCCGCCGCCGCCGCCAGATCGGAGCGCGGCCTCACCGTTGTCAGGTGAGCCCGGTGATCCG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 78.30% 21.70% 0.02% 0.00% NA
All Indica  2759 98.90% 1.10% 0.00% 0.00% NA
All Japonica  1512 36.20% 63.80% 0.07% 0.00% NA
Aus  269 98.50% 1.50% 0.00% 0.00% NA
Indica I  595 97.30% 2.70% 0.00% 0.00% NA
Indica II  465 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 98.50% 1.50% 0.00% 0.00% NA
Temperate Japonica  767 21.80% 78.20% 0.00% 0.00% NA
Tropical Japonica  504 46.60% 53.20% 0.20% 0.00% NA
Japonica Intermediate  241 60.20% 39.80% 0.00% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 74.40% 25.60% 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
vg0910836349 T -> A LOC_Os09g17710.1 upstream_gene_variant ; 4747.0bp to feature; MODIFIER silent_mutation Average:79.538; most accessible tissue: Minghui63 young leaf, score: 89.224 N N N N
vg0910836349 T -> A LOC_Os09g17720.1 downstream_gene_variant ; 2261.0bp to feature; MODIFIER silent_mutation Average:79.538; most accessible tissue: Minghui63 young leaf, score: 89.224 N N N N
vg0910836349 T -> A LOC_Os09g17730.1 intron_variant ; MODIFIER silent_mutation Average:79.538; most accessible tissue: Minghui63 young leaf, score: 89.224 N N N N
vg0910836349 T -> A LOC_Os09g17730.2 intron_variant ; MODIFIER silent_mutation Average:79.538; most accessible tissue: Minghui63 young leaf, score: 89.224 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)
vg0910836349 T A 0.02 0.02 0.03 0.02 0.01 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0910836349 NA 1.55E-11 mr1180 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
vg0910836349 NA 4.68E-13 mr1183 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
vg0910836349 NA 8.89E-06 mr1202 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
vg0910836349 NA 5.57E-13 mr1503 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
vg0910836349 NA 1.46E-06 mr1510 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
vg0910836349 NA 4.36E-08 mr1794 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
vg0910836349 NA 2.31E-12 mr1180_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
vg0910836349 NA 7.71E-11 mr1183_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
vg0910836349 NA 3.67E-07 mr1748_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
vg0910836349 NA 4.11E-13 mr1794_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