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Detailed information for vg1216514861:

Variant ID: vg1216514861 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 16514861
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.81, T: 0.19, others allele: 0.00, population size: 100. )

Flanking Sequence (100 bp) in Reference Genome:


AGTAGTCCAGCCATGGCCAGTGCTATGAGATAGGTTGTCGGTCTTAGTTGGTAGGTTGGGCGCGACGACTCTGCATTTGTTGAGATCGTTCTCGATAATA[T/C]
GGTGTACTCGACCACAACCTACTCGAGTGCTCAACTGTTCCTGAAAAATGTTTTCTAGAAGGCAAGACATATAGCAGGTAATATCGAGTATGTATTCGAA

Reverse complement sequence

TTCGAATACATACTCGATATTACCTGCTATATGTCTTGCCTTCTAGAAAACATTTTTCAGGAACAGTTGAGCACTCGAGTAGGTTGTGGTCGAGTACACC[A/G]
TATTATCGAGAACGATCTCAACAAATGCAGAGTCGTCGCGCCCAACCTACCAACTAAGACCGACAACCTATCTCATAGCACTGGCCATGGCTGGACTACT

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 33.60% 21.20% 0.40% 44.71% NA
All Indica  2759 31.00% 9.00% 0.33% 59.66% NA
All Japonica  1512 34.90% 46.40% 0.40% 18.25% NA
Aus  269 39.40% 7.80% 0.00% 52.79% NA
Indica I  595 12.90% 18.80% 1.01% 67.23% NA
Indica II  465 6.50% 6.70% 0.00% 86.88% NA
Indica III  913 60.10% 4.50% 0.00% 35.38% NA
Indica Intermediate  786 25.40% 8.10% 0.38% 66.03% NA
Temperate Japonica  767 22.70% 76.10% 0.00% 1.17% NA
Tropical Japonica  504 46.20% 4.20% 1.19% 48.41% NA
Japonica Intermediate  241 50.20% 40.20% 0.00% 9.54% NA
VI/Aromatic  96 64.60% 8.30% 3.12% 23.96% NA
Intermediate  90 42.20% 27.80% 1.11% 28.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1216514861 T -> C LOC_Os12g28010.1 missense_variant ; p.His81Arg; MODERATE nonsynonymous_codon ; H81R Average:7.914; most accessible tissue: Callus, score: 23.275 unknown unknown TOLERATED 0.57
vg1216514861 T -> DEL LOC_Os12g28010.1 N frameshift_variant Average:7.914; most accessible tissue: Callus, score: 23.275 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1216514861 NA 7.48E-06 mr1236 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
vg1216514861 3.64E-06 NA mr1778 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
vg1216514861 7.95E-07 NA mr1023_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
vg1216514861 7.16E-06 NA mr1079_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
vg1216514861 1.23E-06 NA mr1132_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
vg1216514861 2.88E-06 NA mr1390_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
vg1216514861 8.68E-10 NA mr1489_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
vg1216514861 2.39E-08 NA mr1778_2 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