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Detailed information for vg0500210699:

Variant ID: vg0500210699 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 210699
Reference Allele: CAlternative Allele: T,G
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.91, T: 0.09, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:


TGATTTCCCTGTGCCCCTTCGTAACTACTCCCTCCGAAAAAAAAAAAAAAAAAAAGGAAAAAAGACAAACCCTGGTTTCCGTGCTTAACGTTTGACCGTT[C/T,G]
ATCTTATTTAAAAAAATTATGAAAAAAATTAAAAAGATAAGTCACACATAAAATATTAATCATGTTTTATCATCTAACAACAATGAAAATACGAATTATA

Reverse complement sequence

TATAATTCGTATTTTCATTGTTGTTAGATGATAAAACATGATTAATATTTTATGTGTGACTTATCTTTTTAATTTTTTTCATAATTTTTTTAAATAAGAT[G/A,C]
AACGGTCAAACGTTAAGCACGGAAACCAGGGTTTGTCTTTTTTCCTTTTTTTTTTTTTTTTTTTCGGAGGGAGTAGTTACGAAGGGGCACAGGGAAATCA

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 46.80% 42.70% 3.77% 6.64% G: 0.04%
All Indica  2759 21.50% 63.50% 4.06% 10.87% G: 0.07%
All Japonica  1512 96.60% 3.40% 0.00% 0.00% NA
Aus  269 6.30% 67.30% 21.93% 4.46% NA
Indica I  595 12.80% 71.60% 5.21% 10.42% NA
Indica II  465 13.80% 62.80% 5.38% 18.06% NA
Indica III  913 34.90% 55.80% 2.41% 6.68% G: 0.22%
Indica Intermediate  786 16.90% 66.90% 4.33% 11.83% NA
Temperate Japonica  767 94.80% 5.20% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 95.40% 4.60% 0.00% 0.00% NA
VI/Aromatic  96 90.60% 7.30% 2.08% 0.00% NA
Intermediate  90 62.20% 30.00% 5.56% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0500210699 C -> T LOC_Os05g01320.1 upstream_gene_variant ; 4943.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0500210699 C -> T LOC_Os05g01330.1 upstream_gene_variant ; 1006.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0500210699 C -> T LOC_Os05g01350.1 upstream_gene_variant ; 2868.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0500210699 C -> T LOC_Os05g01330-LOC_Os05g01350 intergenic_region ; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0500210699 C -> G LOC_Os05g01320.1 upstream_gene_variant ; 4943.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0500210699 C -> G LOC_Os05g01330.1 upstream_gene_variant ; 1006.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0500210699 C -> G LOC_Os05g01350.1 upstream_gene_variant ; 2868.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0500210699 C -> G LOC_Os05g01330-LOC_Os05g01350 intergenic_region ; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0500210699 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)
vg0500210699 C G 0.0 -0.01 0.0 -0.03 -0.02 -0.01
vg0500210699 C T 0.03 0.03 0.02 0.0 0.02 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0500210699 NA 1.65E-11 mr1084 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
vg0500210699 NA 1.12E-08 mr1190 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
vg0500210699 NA 2.23E-12 mr1205 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
vg0500210699 NA 3.35E-06 mr1215 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
vg0500210699 NA 4.41E-06 mr1236 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
vg0500210699 NA 8.07E-07 mr1278 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
vg0500210699 NA 1.07E-06 mr1315 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
vg0500210699 NA 2.44E-14 mr1376 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
vg0500210699 NA 2.44E-14 mr1431 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
vg0500210699 9.96E-06 4.64E-09 mr1445 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
vg0500210699 NA 3.71E-08 mr1506 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
vg0500210699 NA 9.58E-07 mr1516 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
vg0500210699 NA 2.43E-09 mr1776 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
vg0500210699 NA 7.58E-06 mr1898 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
vg0500210699 NA 2.88E-10 mr1921 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
vg0500210699 NA 1.11E-08 mr1986 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