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Detailed information for vg1213849371:

Variant ID: vg1213849371 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 13849371
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 115. )

Flanking Sequence (100 bp) in Reference Genome:


GCGAGCAGCCTAGGAGAGGAAACAACGCAGCTTTGCGATGGATCGGCAGAAGGGAAGCGGAAGAGGGGTGTGCGTTGAGGGAGAAGGCGGTGAACGCGCG[C/T]
GGGGGACGGGGGAGGAGAAGCGAGCGTGGCCGGGCTAGTGGGGAGAGCGACCGGTGGCGGGCCCGTGCCTGGCGCGCGTGGCGGCTGGTGGGGAGGGGAG

Reverse complement sequence

CTCCCCTCCCCACCAGCCGCCACGCGCGCCAGGCACGGGCCCGCCACCGGTCGCTCTCCCCACTAGCCCGGCCACGCTCGCTTCTCCTCCCCCGTCCCCC[G/A]
CGCGCGTTCACCGCCTTCTCCCTCAACGCACACCCCTCTTCCGCTTCCCTTCTGCCGATCCATCGCAAAGCTGCGTTGTTTCCTCTCCTAGGCTGCTCGC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 69.10% 30.80% 0.06% 0.00% NA
All Indica  2759 49.30% 50.70% 0.04% 0.00% NA
All Japonica  1512 98.40% 1.50% 0.13% 0.00% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 28.10% 71.90% 0.00% 0.00% NA
Indica II  465 72.50% 27.50% 0.00% 0.00% NA
Indica III  913 45.30% 54.70% 0.00% 0.00% NA
Indica Intermediate  786 56.10% 43.80% 0.13% 0.00% NA
Temperate Japonica  767 98.40% 1.40% 0.13% 0.00% NA
Tropical Japonica  504 98.20% 1.60% 0.20% 0.00% NA
Japonica Intermediate  241 98.80% 1.20% 0.00% 0.00% NA
VI/Aromatic  96 84.40% 15.60% 0.00% 0.00% NA
Intermediate  90 81.10% 18.90% 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
vg1213849371 C -> T LOC_Os12g24270-LOC_Os12g24290 intergenic_region ; MODIFIER silent_mutation Average:64.346; most accessible tissue: Zhenshan97 young leaf, score: 88.637 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1213849371 NA 3.06E-06 Spikelet_length Ind_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg1213849371 NA 6.03E-08 mr1308 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
vg1213849371 NA 5.98E-13 mr1531 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
vg1213849371 NA 1.75E-07 mr1707 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
vg1213849371 6.07E-06 NA mr1853 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
vg1213849371 1.13E-06 1.13E-06 mr1853 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
vg1213849371 NA 8.68E-10 mr1860 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
vg1213849371 NA 3.91E-07 mr1308_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
vg1213849371 NA 1.44E-06 mr1361_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
vg1213849371 NA 5.27E-08 mr1707_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
vg1213849371 3.92E-06 3.92E-06 mr1853_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
vg1213849371 NA 4.43E-10 mr1860_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