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Detailed information for vg0503843986:

Variant ID: vg0503843986 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 3843986
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.94, T: 0.06, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:


GCCGTCGTCACTACCCCCATGGTGCCAGCAACGGGCAGCTGGCGTGCGGCGGCGGCGGCGGCGAGGAGGTGCGAGGCGTGGGAGGAAGGGAGCACGGCGG[C/T]
GGCGGAGGGGAGGCGGTACTTGTGCCTGACGATGTCGGCGCGGACGGCGGCGAGCTCGGCCTCGAGGGCCTGGACCTGCTGCTGCAAGGTGAGGATGGCG

Reverse complement sequence

CGCCATCCTCACCTTGCAGCAGCAGGTCCAGGCCCTCGAGGCCGAGCTCGCCGCCGTCCGCGCCGACATCGTCAGGCACAAGTACCGCCTCCCCTCCGCC[G/A]
CCGCCGTGCTCCCTTCCTCCCACGCCTCGCACCTCCTCGCCGCCGCCGCCGCCGCACGCCAGCTGCCCGTTGCTGGCACCATGGGGGTAGTGACGACGGC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 50.60% 49.30% 0.13% 0.00% NA
All Indica  2759 83.50% 16.30% 0.18% 0.00% NA
All Japonica  1512 1.20% 98.70% 0.07% 0.00% NA
Aus  269 10.40% 89.60% 0.00% 0.00% NA
Indica I  595 94.80% 5.00% 0.17% 0.00% NA
Indica II  465 74.40% 24.90% 0.65% 0.00% NA
Indica III  913 86.00% 14.00% 0.00% 0.00% NA
Indica Intermediate  786 77.50% 22.40% 0.13% 0.00% NA
Temperate Japonica  767 1.70% 98.30% 0.00% 0.00% NA
Tropical Japonica  504 0.40% 99.40% 0.20% 0.00% NA
Japonica Intermediate  241 1.20% 98.80% 0.00% 0.00% NA
VI/Aromatic  96 9.40% 90.60% 0.00% 0.00% NA
Intermediate  90 34.40% 65.60% 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
vg0503843986 C -> T LOC_Os05g07270.1 missense_variant ; p.Ala138Thr; MODERATE nonsynonymous_codon ; A138T Average:84.298; most accessible tissue: Zhenshan97 root, score: 89.403 unknown unknown TOLERATED 0.27

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)
vg0503843986 C T -0.01 0.0 -0.01 -0.01 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0503843986 NA 1.79E-13 mr1938 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
vg0503843986 2.39E-06 7.24E-07 mr1238_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
vg0503843986 NA 1.05E-13 mr1514_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
vg0503843986 NA 4.00E-32 mr1598_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
vg0503843986 NA 1.71E-06 mr1841_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