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Detailed information for vg1220167325:

Variant ID: vg1220167325 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 20167325
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 59. )

Flanking Sequence (100 bp) in Reference Genome:


CTGCGTCCGACTGGTTTCCAGTCGGGGGCTCTTGAGTTGTTGCCGTTTCAGTTGTTGCCGACTGGTTTCCAGTCGGCGGCAGGTCACTCGGATCGGCCCT[A/G]
TCGCCCGAAGCATGGGCACCAGTCGGCTGGCTTTCAGTGGTCGGCTGGTTTTCAACAGTCGGCTCGGGGTCCTTGGATATATTTTGCTCTGTCATGCCAG

Reverse complement sequence

CTGGCATGACAGAGCAAAATATATCCAAGGACCCCGAGCCGACTGTTGAAAACCAGCCGACCACTGAAAGCCAGCCGACTGGTGCCCATGCTTCGGGCGA[T/C]
AGGGCCGATCCGAGTGACCTGCCGCCGACTGGAAACCAGTCGGCAACAACTGAAACGGCAACAACTCAAGAGCCCCCGACTGGAAACCAGTCGGACGCAG

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 24.00% 6.70% 49.81% 19.49% NA
All Indica  2759 3.70% 10.10% 69.74% 16.46% NA
All Japonica  1512 64.30% 1.10% 14.09% 20.57% NA
Aus  269 8.20% 7.10% 39.78% 44.98% NA
Indica I  595 5.00% 13.30% 47.56% 34.12% NA
Indica II  465 4.50% 8.60% 77.42% 9.46% NA
Indica III  913 2.50% 8.40% 82.58% 6.46% NA
Indica Intermediate  786 3.60% 10.60% 67.05% 18.83% NA
Temperate Japonica  767 93.10% 0.00% 2.74% 4.17% NA
Tropical Japonica  504 21.80% 2.80% 32.34% 43.06% NA
Japonica Intermediate  241 61.40% 0.80% 12.03% 25.73% NA
VI/Aromatic  96 5.20% 2.10% 67.71% 25.00% NA
Intermediate  90 35.60% 2.20% 50.00% 12.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1220167325 A -> DEL LOC_Os12g33340.1 N frameshift_variant Average:19.0; most accessible tissue: Minghui63 young leaf, score: 40.718 N N N N
vg1220167325 A -> G LOC_Os12g33340.1 synonymous_variant ; p.Asp438Asp; LOW synonymous_codon Average:19.0; most accessible tissue: Minghui63 young leaf, score: 40.718 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1220167325 4.07E-06 3.31E-07 mr1224 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
vg1220167325 NA 1.93E-08 mr1593 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