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Detailed information for vg1216422905:

Variant ID: vg1216422905 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 16422905
Reference Allele: TAlternative Allele: A
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.96, T: 0.04, others allele: 0.00, population size: 84. )

Flanking Sequence (100 bp) in Reference Genome:


CCGTAGAGGCGAGGGCACTAGTCAGCTGCAGACGAGATGACCGGCGGTGAAGACGATAAGGCCAATCAACACTAGCAGAATCATGCAGCCATGGAAGTGA[T/A]
GAAACCAATCGACAGCAGACGTAGACAGCTTGCGTTGAAGATGATGACGCCTATTAGCGGCGACGGCGACGTGGCCAGCTGTGAAGACAATAGCTCCAGT

Reverse complement sequence

ACTGGAGCTATTGTCTTCACAGCTGGCCACGTCGCCGTCGCCGCTAATAGGCGTCATCATCTTCAACGCAAGCTGTCTACGTCTGCTGTCGATTGGTTTC[A/T]
TCACTTCCATGGCTGCATGATTCTGCTAGTGTTGATTGGCCTTATCGTCTTCACCGCCGGTCATCTCGTCTGCAGCTGACTAGTGCCCTCGCCTCTACGG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 17.20% 16.90% 0.78% 65.13% NA
All Indica  2759 10.00% 2.30% 1.09% 86.63% NA
All Japonica  1512 30.40% 46.80% 0.26% 22.49% NA
Aus  269 8.90% 0.70% 0.00% 90.33% NA
Indica I  595 0.70% 1.50% 0.84% 96.97% NA
Indica II  465 29.20% 3.00% 1.94% 65.81% NA
Indica III  913 6.00% 0.50% 0.11% 93.32% NA
Indica Intermediate  786 10.30% 4.50% 1.91% 83.33% NA
Temperate Japonica  767 12.00% 76.40% 0.13% 11.47% NA
Tropical Japonica  504 56.90% 4.60% 0.20% 38.29% NA
Japonica Intermediate  241 33.60% 41.10% 0.83% 24.48% NA
VI/Aromatic  96 26.00% 1.00% 1.04% 71.88% NA
Intermediate  90 32.20% 25.60% 2.22% 40.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1216422905 T -> DEL LOC_Os12g27860.1 N frameshift_variant Average:44.965; most accessible tissue: Minghui63 flag leaf, score: 72.472 N N N N
vg1216422905 T -> A LOC_Os12g27860.1 missense_variant ; p.Met4Lys; MODERATE nonsynonymous_codon ; M4K Average:44.965; most accessible tissue: Minghui63 flag leaf, score: 72.472 unknown unknown TOLERATED 1.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1216422905 NA 2.16E-10 mr1089_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
vg1216422905 NA 1.39E-06 mr1097_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
vg1216422905 NA 5.64E-08 mr1129_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
vg1216422905 2.13E-06 NA mr1201_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
vg1216422905 NA 6.49E-07 mr1257_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
vg1216422905 NA 6.98E-06 mr1404_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