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Detailed information for vg1125498126:

Variant ID: vg1125498126 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 25498126
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 96. )

Flanking Sequence (100 bp) in Reference Genome:


CATCTGGATGCTCAAGGCCAAGGCAGGCAGGGACGTCGCCAAGAGGGACGCCGCGGCGAGGGCGCTTGCCGCACTCGTCGCAGCGAGCAGCTACAAAAAA[T/A]
TTTCAAGAAAGAGGAGCAAGGCATCATCAATGTCGTCCAGCTGCTCGACCCGAGCACCGCCCGCGGCGGCATTGACGCGTGGTTCCCGGTGTCCGTGCTG

Reverse complement sequence

CAGCACGGACACCGGGAACCACGCGTCAATGCCGCCGCGGGCGGTGCTCGGGTCGAGCAGCTGGACGACATTGATGATGCCTTGCTCCTCTTTCTTGAAA[A/T]
TTTTTTGTAGCTGCTCGCTGCGACGAGTGCGGCAAGCGCCCTCGCCGCGGCGTCCCTCTTGGCGACGTCCCTGCCTGCCTTGGCCTTGAGCATCCAGATG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 75.20% 11.30% 0.87% 12.67% NA
All Indica  2759 70.60% 13.70% 0.80% 14.86% NA
All Japonica  1512 79.60% 9.20% 1.06% 10.19% NA
Aus  269 88.80% 0.00% 1.12% 10.04% NA
Indica I  595 53.60% 38.70% 1.01% 6.72% NA
Indica II  465 68.00% 19.40% 0.65% 12.04% NA
Indica III  913 79.40% 0.10% 0.66% 19.82% NA
Indica Intermediate  786 74.90% 7.30% 0.89% 16.92% NA
Temperate Japonica  767 88.40% 9.30% 0.78% 1.56% NA
Tropical Japonica  504 71.00% 7.70% 0.99% 20.24% NA
Japonica Intermediate  241 69.30% 12.00% 2.07% 16.60% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 74.40% 16.70% 0.00% 8.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1125498126 T -> A LOC_Os11g42360.1 missense_variant ; p.Phe96Ile; MODERATE nonsynonymous_codon ; F96I Average:49.959; most accessible tissue: Zhenshan97 flag leaf, score: 95.83 unknown unknown TOLERATED 0.21
vg1125498126 T -> DEL LOC_Os11g42360.1 N frameshift_variant Average:49.959; most accessible tissue: Zhenshan97 flag leaf, score: 95.83 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)
vg1125498126 T A 0.01 -0.01 0.0 0.0 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1125498126 3.70E-09 2.61E-13 mr1191 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
vg1125498126 7.37E-12 8.90E-15 mr1191 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
vg1125498126 8.58E-06 1.10E-08 mr1530 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
vg1125498126 5.61E-10 2.73E-15 mr1644 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
vg1125498126 7.87E-13 3.28E-17 mr1644 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
vg1125498126 NA 1.50E-08 mr1662 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
vg1125498126 5.39E-10 7.93E-16 mr1662 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
vg1125498126 NA 2.92E-09 mr1745 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
vg1125498126 NA 6.77E-06 mr1133_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
vg1125498126 1.12E-07 1.78E-20 mr1191_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
vg1125498126 1.53E-14 6.46E-24 mr1191_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
vg1125498126 3.42E-07 1.81E-13 mr1530_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
vg1125498126 NA 4.44E-09 mr1662_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
vg1125498126 4.90E-09 6.26E-17 mr1662_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
vg1125498126 NA 1.31E-13 mr1745_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