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Detailed information for vg0626222999:

Variant ID: vg0626222999 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 26222999
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, G: 0.00, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:


TTTGGTTTGTGTATTAGATGTGATATGTTGTATGCGTTGCCTTTTAATTAATAAGAAGACGATGACATGGTCCAAATTAGATCTGACATCCACCTCCACT[A/G]
TAAAACTTACCCTGAACGTACGTACATGCCCCCACACGCCATCACGGACGCGTGCGCCGACGTACGTCCGATGCGGTGCGAGCGCGGGTGCGTACGTGCT

Reverse complement sequence

AGCACGTACGCACCCGCGCTCGCACCGCATCGGACGTACGTCGGCGCACGCGTCCGTGATGGCGTGTGGGGGCATGTACGTACGTTCAGGGTAAGTTTTA[T/C]
AGTGGAGGTGGATGTCAGATCTAATTTGGACCATGTCATCGTCTTCTTATTAATTAAAAGGCAACGCATACAACATATCACATCTAATACACAAACCAAA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 78.90% 20.50% 0.53% 0.00% NA
All Indica  2759 97.60% 2.40% 0.00% 0.00% NA
All Japonica  1512 42.80% 55.70% 1.52% 0.00% NA
Aus  269 98.50% 1.50% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 95.70% 4.30% 0.00% 0.00% NA
Indica III  913 99.30% 0.70% 0.00% 0.00% NA
Indica Intermediate  786 95.00% 5.00% 0.00% 0.00% NA
Temperate Japonica  767 61.40% 36.90% 1.69% 0.00% NA
Tropical Japonica  504 20.60% 78.20% 1.19% 0.00% NA
Japonica Intermediate  241 29.90% 68.50% 1.66% 0.00% NA
VI/Aromatic  96 67.70% 32.30% 0.00% 0.00% NA
Intermediate  90 66.70% 31.10% 2.22% 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
vg0626222999 A -> G LOC_Os06g43600.1 upstream_gene_variant ; 4105.0bp to feature; MODIFIER silent_mutation Average:83.745; most accessible tissue: Minghui63 panicle, score: 98.566 N N N N
vg0626222999 A -> G LOC_Os06g43600.2 upstream_gene_variant ; 4105.0bp to feature; MODIFIER silent_mutation Average:83.745; most accessible tissue: Minghui63 panicle, score: 98.566 N N N N
vg0626222999 A -> G LOC_Os06g43590.2 downstream_gene_variant ; 4333.0bp to feature; MODIFIER silent_mutation Average:83.745; most accessible tissue: Minghui63 panicle, score: 98.566 N N N N
vg0626222999 A -> G LOC_Os06g43590.4 downstream_gene_variant ; 4333.0bp to feature; MODIFIER silent_mutation Average:83.745; most accessible tissue: Minghui63 panicle, score: 98.566 N N N N
vg0626222999 A -> G LOC_Os06g43590-LOC_Os06g43600 intergenic_region ; MODIFIER silent_mutation Average:83.745; most accessible tissue: Minghui63 panicle, score: 98.566 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)
vg0626222999 A G -0.33 -0.21 -0.07 0.07 -0.07 -0.1

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0626222999 NA 1.28E-11 mr1070 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
vg0626222999 NA 8.62E-10 mr1097 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
vg0626222999 NA 2.32E-07 mr1182 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
vg0626222999 NA 1.36E-06 mr1282 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
vg0626222999 NA 4.07E-08 mr1442 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
vg0626222999 NA 5.19E-06 mr1650 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
vg0626222999 NA 6.29E-06 mr1182_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
vg0626222999 6.01E-08 NA mr1768_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
vg0626222999 7.72E-06 2.57E-06 mr1768_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
vg0626222999 NA 4.09E-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