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Detailed information for vg0702825530:

Variant ID: vg0702825530 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 2825530
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 322. )

Flanking Sequence (100 bp) in Reference Genome:


GGCATGGCAGGAATTGTATGCCAGGTCAAGTAGTTCAGGTCCAGCACCTTCCACTGTATCTTACCAGTGCAACGGTGGAAAGCCAGGGTGAACAACAACG[G/C]
TGACCGAAAACCCATCACCTTCCTCTGCATGAAGAACCGCGCCTTGTCAGCTAGGAGGTGATGCCACCGGCGACACACAAGCCTGCATGCCTCATGGGTC

Reverse complement sequence

GACCCATGAGGCATGCAGGCTTGTGTGTCGCCGGTGGCATCACCTCCTAGCTGACAAGGCGCGGTTCTTCATGCAGAGGAAGGTGATGGGTTTTCGGTCA[C/G]
CGTTGTTGTTCACCCTGGCTTTCCACCGTTGCACTGGTAAGATACAGTGGAAGGTGCTGGACCTGAACTACTTGACCTGGCATACAATTCCTGCCATGCC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 96.20% 3.00% 0.80% 0.00% NA
All Indica  2759 93.70% 5.00% 1.38% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 80.00% 15.00% 5.04% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.50% 0.50% 0.00% 0.00% NA
Indica Intermediate  786 93.50% 5.50% 1.02% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 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
vg0702825530 G -> C LOC_Os07g05880.1 missense_variant ; p.Pro106Ala; MODERATE nonsynonymous_codon ; P106A Average:90.063; most accessible tissue: Minghui63 flag leaf, score: 96.084 possibly damaging 1.523 DELETERIOUS 0.04
vg0702825530 G -> C LOC_Os07g05880.2 missense_variant ; p.Pro106Ala; MODERATE nonsynonymous_codon ; P106A Average:90.063; most accessible tissue: Minghui63 flag leaf, score: 96.084 possibly damaging 1.523 DELETERIOUS 0.04

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)
vg0702825530 G C 0.05 0.02 0.02 0.02 0.01 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0702825530 NA 2.45E-08 mr1739 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
vg0702825530 NA 1.97E-06 mr1358_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
vg0702825530 3.36E-06 4.00E-11 mr1739_2 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