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Detailed information for vg1001500421:

Variant ID: vg1001500421 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 1500421
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.79, C: 0.20, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:


TTAGTTACACGTCTCCGTAAAAAAATCCCGAAAAGAAAAAAAGAAACCGCAAAAAACACTCTAACCACTCCGCCTCGCGCGCGAATTAGCTTTCTCGAAT[C/T]
AGTGATTAACTCTAATCACCGTAATTAACGCTAATCGCCATGATTAGTGATGGGAGCACGACGGGGTTCGCTCTGCAGCCTAACACGTGGCAGTGCGCGT

Reverse complement sequence

ACGCGCACTGCCACGTGTTAGGCTGCAGAGCGAACCCCGTCGTGCTCCCATCACTAATCATGGCGATTAGCGTTAATTACGGTGATTAGAGTTAATCACT[G/A]
ATTCGAGAAAGCTAATTCGCGCGCGAGGCGGAGTGGTTAGAGTGTTTTTTGCGGTTTCTTTTTTTCTTTTCGGGATTTTTTTACGGAGACGTGTAACTAA

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 70.80% 29.10% 0.13% 0.00% NA
All Indica  2759 60.70% 39.10% 0.22% 0.00% NA
All Japonica  1512 94.60% 5.40% 0.00% 0.00% NA
Aus  269 31.60% 68.40% 0.00% 0.00% NA
Indica I  595 59.30% 40.30% 0.34% 0.00% NA
Indica II  465 69.20% 30.80% 0.00% 0.00% NA
Indica III  913 56.00% 43.90% 0.11% 0.00% NA
Indica Intermediate  786 62.20% 37.40% 0.38% 0.00% NA
Temperate Japonica  767 99.00% 1.00% 0.00% 0.00% NA
Tropical Japonica  504 86.70% 13.30% 0.00% 0.00% NA
Japonica Intermediate  241 97.50% 2.50% 0.00% 0.00% NA
VI/Aromatic  96 88.50% 11.50% 0.00% 0.00% NA
Intermediate  90 77.80% 22.20% 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
vg1001500421 C -> T LOC_Os10g03480.1 upstream_gene_variant ; 1252.0bp to feature; MODIFIER silent_mutation Average:87.635; most accessible tissue: Zhenshan97 young leaf, score: 97.304 N N N N
vg1001500421 C -> T LOC_Os10g03490.1 downstream_gene_variant ; 858.0bp to feature; MODIFIER silent_mutation Average:87.635; most accessible tissue: Zhenshan97 young leaf, score: 97.304 N N N N
vg1001500421 C -> T LOC_Os10g03480-LOC_Os10g03490 intergenic_region ; MODIFIER silent_mutation Average:87.635; most accessible tissue: Zhenshan97 young leaf, score: 97.304 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)
vg1001500421 C T -0.09 -0.01 -0.04 -0.04 -0.08 -0.07

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1001500421 9.43E-07 NA mr1486 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
vg1001500421 3.84E-09 1.04E-12 mr1486 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
vg1001500421 2.92E-07 5.20E-09 mr1548 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
vg1001500421 NA 8.27E-06 mr1588 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
vg1001500421 8.00E-06 NA mr1721 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
vg1001500421 NA 6.95E-08 mr1721 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
vg1001500421 7.85E-08 9.84E-12 mr1486_2 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
vg1001500421 5.97E-08 NA mr1721_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
vg1001500421 5.24E-07 7.03E-10 mr1721_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