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Detailed information for vg1005164238:

Variant ID: vg1005164238 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 5164238
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 39. )

Flanking Sequence (100 bp) in Reference Genome:


CTTCTGTAGAGAAATTGTACCATGACTTCTCCACCAGCATGGCATATGAGCATGGATAGGTTCTCCACTTGCTGTTGTTCCTGTGCTGGAATCTCACAAG[A/G]
GTCGTGTTGACGCCAGGAGGCAGTGTCTGCTGGCAGCAGCCAAGCCCCGTGGCATTCTCGCACGGTCCATTCCTCGCCTTGGACACTGAACTGAGGAAAG

Reverse complement sequence

CTTTCCTCAGTTCAGTGTCCAAGGCGAGGAATGGACCGTGCGAGAATGCCACGGGGCTTGGCTGCTGCCAGCAGACACTGCCTCCTGGCGTCAACACGAC[T/C]
CTTGTGAGATTCCAGCACAGGAACAACAGCAAGTGGAGAACCTATCCATGCTCATATGCCATGCTGGTGGAGAAGTCATGGTACAATTTCTCTACAGAAG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 63.20% 27.00% 1.25% 8.51% NA
All Indica  2759 87.20% 4.70% 1.63% 6.49% NA
All Japonica  1512 16.30% 68.70% 0.86% 14.09% NA
Aus  269 98.50% 1.50% 0.00% 0.00% NA
Indica I  595 92.60% 6.70% 0.00% 0.67% NA
Indica II  465 83.90% 5.80% 1.29% 9.03% NA
Indica III  913 82.60% 2.10% 3.40% 11.94% NA
Indica Intermediate  786 90.30% 5.60% 1.02% 3.05% NA
Temperate Japonica  767 12.40% 81.70% 0.26% 5.61% NA
Tropical Japonica  504 20.20% 54.60% 2.18% 23.02% NA
Japonica Intermediate  241 20.70% 56.80% 0.00% 22.41% NA
VI/Aromatic  96 25.00% 66.70% 1.04% 7.29% NA
Intermediate  90 53.30% 43.30% 0.00% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1005164238 A -> G LOC_Os10g09570.1 synonymous_variant ; p.Thr232Thr; LOW synonymous_codon Average:86.732; most accessible tissue: Callus, score: 98.666 N N N N
vg1005164238 A -> DEL LOC_Os10g09570.1 N frameshift_variant Average:86.732; most accessible tissue: Callus, score: 98.666 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)
vg1005164238 A G 0.0 0.02 0.01 0.02 0.02 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1005164238 NA 9.17E-08 mr1709 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
vg1005164238 NA 1.03E-06 mr1379_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
vg1005164238 NA 1.28E-06 mr1409_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
vg1005164238 4.95E-07 4.94E-07 mr1547_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
vg1005164238 NA 7.51E-06 mr1559_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
vg1005164238 NA 2.97E-08 mr1709_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