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Detailed information for vg0431857957:

Variant ID: vg0431857957 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 31857957
Reference Allele: AAlternative Allele: G,C
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.91, A: 0.08, others allele: 0.00, population size: 186. )

Flanking Sequence (100 bp) in Reference Genome:


TCCAGTTGAGTACCTATCTATTTCTAGCTACCATGGAAGTGGGAAAGCATTGTCACAGCTTCTCTCTCATCTCCCAAAGCTCTCAGAGTTGTATCTTATG[A/G,C]
ACTGCAACAAGATTACACGGATGTGTATAGCTGTAGAACAGCAGCAAACAACTGCTGTTGAGCTGGAGGATACACAAGCAGTCGAATCTATTCAGCAGCA

Reverse complement sequence

TGCTGCTGAATAGATTCGACTGCTTGTGTATCCTCCAGCTCAACAGCAGTTGTTTGCTGCTGTTCTACAGCTATACACATCCGTGTAATCTTGTTGCAGT[T/C,G]
CATAAGATACAACTCTGAGAGCTTTGGGAGATGAGAGAGAAGCTGTGACAATGCTTTCCCACTTCCATGGTAGCTAGAAATAGATAGGTACTCAACTGGA

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 57.20% 35.60% 1.38% 5.84% C: 0.04%
All Indica  2759 61.30% 29.10% 1.52% 8.16% NA
All Japonica  1512 43.10% 55.20% 0.86% 0.86% NA
Aus  269 92.20% 4.50% 1.12% 2.23% NA
Indica I  595 42.40% 56.50% 0.50% 0.67% NA
Indica II  465 53.50% 39.60% 0.86% 6.02% NA
Indica III  913 78.50% 3.70% 2.52% 15.22% NA
Indica Intermediate  786 60.10% 31.60% 1.53% 6.87% NA
Temperate Japonica  767 16.90% 82.10% 0.91% 0.00% NA
Tropical Japonica  504 72.40% 24.60% 0.99% 1.98% NA
Japonica Intermediate  241 65.10% 33.20% 0.41% 1.24% NA
VI/Aromatic  96 65.60% 6.20% 5.21% 22.92% NA
Intermediate  90 53.30% 31.10% 2.22% 11.11% C: 2.22%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0431857957 A -> C LOC_Os04g53496.1 missense_variant ; p.Asn1177His; MODERATE nonsynonymous_codon Average:82.536; most accessible tissue: Minghui63 panicle, score: 95.468 benign 0.011 TOLERATED 0.72
vg0431857957 A -> DEL LOC_Os04g53496.1 N frameshift_variant Average:82.536; most accessible tissue: Minghui63 panicle, score: 95.468 N N N N
vg0431857957 A -> G LOC_Os04g53496.1 missense_variant ; p.Asn1177Asp; MODERATE nonsynonymous_codon Average:82.536; most accessible tissue: Minghui63 panicle, score: 95.468 benign 0.633 TOLERATED 0.57
vg0431857957 A -> G LOC_Os04g53496.1 missense_variant ; p.Asn1177Asp; MODERATE nonsynonymous_codon Average:82.536; most accessible tissue: Minghui63 panicle, score: 95.468 benign -0.222 TOLERATED 0.81
vg0431857957 A -> G LOC_Os04g53496.1 missense_variant ; p.Asn1177Asp; MODERATE nonsynonymous_codon Average:82.536; most accessible tissue: Minghui63 panicle, score: 95.468 benign -0.06 TOLERATED 0.38

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)
vg0431857957 A C -0.07 -0.01 -0.01 0.0 -0.01 -0.02
vg0431857957 A G -0.18 -0.04 -0.05 -0.04 -0.06 -0.07

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0431857957 NA 1.47E-13 Heading_date All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0431857957 2.61E-06 NA mr1003 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
vg0431857957 NA 3.07E-06 mr1729 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
vg0431857957 NA 5.48E-06 mr1928 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
vg0431857957 NA 6.47E-06 mr1051_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
vg0431857957 NA 4.47E-07 mr1229_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
vg0431857957 NA 1.29E-07 mr1521_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
vg0431857957 NA 1.71E-07 mr1880_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
vg0431857957 NA 1.13E-07 mr1952_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