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Detailed information for vg1105431576:

Variant ID: vg1105431576 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 5431576
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.64, G: 0.36, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:


TCTGCTAATCATCGATAAGCATATACAAGCATGCTTGCTGGGCACACAAGTATAGATTAAGACCTTTTCAGGGAATATTTTTTCACCATCCTAATCATGC[G/C]
AATTAATTAGTTTCATGACTATAACTACTTGAGAAGTAGTGCATCTGAAAAAACCATATAAAAGGGAGTGACCTTTCTTTACTCCATTTCCCTCCATATT

Reverse complement sequence

AATATGGAGGGAAATGGAGTAAAGAAAGGTCACTCCCTTTTATATGGTTTTTTCAGATGCACTACTTCTCAAGTAGTTATAGTCATGAAACTAATTAATT[C/G]
GCATGATTAGGATGGTGAAAAAATATTCCCTGAAAAGGTCTTAATCTATACTTGTGTGCCCAGCAAGCATGCTTGTATATGCTTATCGATGATTAGCAGA

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 62.20% 37.70% 0.13% 0.00% NA
All Indica  2759 46.50% 53.40% 0.11% 0.00% NA
All Japonica  1512 90.60% 9.30% 0.13% 0.00% NA
Aus  269 52.40% 47.60% 0.00% 0.00% NA
Indica I  595 56.60% 43.40% 0.00% 0.00% NA
Indica II  465 83.00% 16.80% 0.22% 0.00% NA
Indica III  913 24.50% 75.40% 0.11% 0.00% NA
Indica Intermediate  786 42.90% 57.00% 0.13% 0.00% NA
Temperate Japonica  767 99.10% 0.80% 0.13% 0.00% NA
Tropical Japonica  504 76.00% 23.80% 0.20% 0.00% NA
Japonica Intermediate  241 94.20% 5.80% 0.00% 0.00% NA
VI/Aromatic  96 87.50% 12.50% 0.00% 0.00% NA
Intermediate  90 66.70% 32.20% 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
vg1105431576 G -> C LOC_Os11g10070.1 downstream_gene_variant ; 4399.0bp to feature; MODIFIER silent_mutation Average:72.599; most accessible tissue: Zhenshan97 root, score: 89.659 N N N N
vg1105431576 G -> C LOC_Os11g10070-LOC_Os11g10080 intergenic_region ; MODIFIER silent_mutation Average:72.599; most accessible tissue: Zhenshan97 root, score: 89.659 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)
vg1105431576 G C 0.08 -0.04 -0.04 0.0 0.04 0.09

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1105431576 NA 1.54E-07 mr1042 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
vg1105431576 NA 4.09E-06 mr1042 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
vg1105431576 NA 1.88E-07 mr1043 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
vg1105431576 NA 4.31E-06 mr1043 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
vg1105431576 NA 1.85E-07 mr1185 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
vg1105431576 NA 7.69E-08 mr1269 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
vg1105431576 NA 1.67E-06 mr1677 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
vg1105431576 NA 1.48E-07 mr1975 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
vg1105431576 NA 5.66E-08 mr1063_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
vg1105431576 NA 3.91E-07 mr1330_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
vg1105431576 NA 1.41E-07 mr1510_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
vg1105431576 NA 7.81E-06 mr1806_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