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Detailed information for vg1127678631:

Variant ID: vg1127678631 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 27678631
Reference Allele: CAlternative Allele: G
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, G: 0.03, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:


CTAAATCCAGCGTGGATCTGAGATCTAGAGCTGTGCTAGATGAGGCCTTGACATCTTTTTCAAAGACTAAATAGGCCTACTTCTGTTATGAATTTTTTTC[C/G]
TCATTTAAAATCTTTTTAGTGTGACTTGTTTGACACTTTGACTCGATTTAAGAATGTGATGTTGCTGGGAGAGCATATATCTAAAAGAGAAGTACATGTT

Reverse complement sequence

AACATGTACTTCTCTTTTAGATATATGCTCTCCCAGCAACATCACATTCTTAAATCGAGTCAAAGTGTCAAACAAGTCACACTAAAAAGATTTTAAATGA[G/C]
GAAAAAAATTCATAACAGAAGTAGGCCTATTTAGTCTTTGAAAAAGATGTCAAGGCCTCATCTAGCACAGCTCTAGATCTCAGATCCACGCTGGATTTAG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 89.40% 10.60% 0.06% 0.00% NA
All Indica  2759 91.40% 8.50% 0.07% 0.00% NA
All Japonica  1512 87.80% 12.20% 0.00% 0.00% NA
Aus  269 72.90% 27.10% 0.00% 0.00% NA
Indica I  595 70.10% 29.70% 0.17% 0.00% NA
Indica II  465 98.50% 1.50% 0.00% 0.00% NA
Indica III  913 98.50% 1.50% 0.00% 0.00% NA
Indica Intermediate  786 95.20% 4.70% 0.13% 0.00% NA
Temperate Japonica  767 93.50% 6.50% 0.00% 0.00% NA
Tropical Japonica  504 78.40% 21.60% 0.00% 0.00% NA
Japonica Intermediate  241 89.20% 10.80% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 92.20% 6.70% 1.11% 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
vg1127678631 C -> G LOC_Os11g45740-LOC_Os11g45750 intergenic_region ; MODIFIER silent_mutation Average:60.097; most accessible tissue: Minghui63 root, score: 87.205 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)
vg1127678631 C G 0.03 -0.01 -0.02 0.0 0.0 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1127678631 5.45E-06 2.21E-07 mr1295 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
vg1127678631 NA 7.48E-08 mr1592 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
vg1127678631 NA 1.13E-06 mr1909 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
vg1127678631 NA 2.72E-06 mr1921 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
vg1127678631 NA 5.42E-06 mr1224_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