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Detailed information for vg1224449038:

Variant ID: vg1224449038 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 24449038
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:


CAAGAGGTTGGAGTATAACGCCAACCTCCCTGGATCTAGATCGGATCGGGGCTAAAGCCGGAGCTCGCCTAGATCTTCGAGTGGGAGATGTCTTGACTGT[G/A]
AAGACAGCGGCCAAATCATCAGGAAGTTTCATCAGGATTGAGGGATAGGACCCGTCGTCTTGATCTGGTCGTGGAAAAATAGATTGGATCTCGTCCGAGT

Reverse complement sequence

ACTCGGACGAGATCCAATCTATTTTTCCACGACCAGATCAAGACGACGGGTCCTATCCCTCAATCCTGATGAAACTTCCTGATGATTTGGCCGCTGTCTT[C/T]
ACAGTCAAGACATCTCCCACTCGAAGATCTAGGCGAGCTCCGGCTTTAGCCCCGATCCGATCTAGATCCAGGGAGGTTGGCGTTATACTCCAACCTCTTG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 96.90% 0.10% 1.59% 1.42% NA
All Indica  2759 94.70% 0.10% 2.68% 2.43% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 94.60% 0.00% 4.20% 1.18% NA
Indica II  465 96.30% 0.20% 1.72% 1.72% NA
Indica III  913 93.10% 0.00% 2.63% 4.27% NA
Indica Intermediate  786 95.80% 0.40% 2.16% 1.65% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 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 98.90% 0.00% 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
vg1224449038 G -> DEL LOC_Os12g39610.1 N frameshift_variant Average:68.141; most accessible tissue: Zhenshan97 flag leaf, score: 84.998 N N N N
vg1224449038 G -> A LOC_Os12g39610.1 synonymous_variant ; p.Phe106Phe; LOW synonymous_codon Average:68.141; most accessible tissue: Zhenshan97 flag leaf, score: 84.998 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1224449038 3.86E-06 3.86E-06 mr1194 Ind_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
vg1224449038 7.20E-07 8.84E-07 mr1748_2 Ind_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