Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg1217338702:

Variant ID: vg1217338702 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 17338702
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AACCGGACACATTCTTCACCCCCAACTACGCAAGCCGAACAAATAACCCCCTCCCTGCCCCGGCCTCAAACCATGGTGGTTTTGTCCTACGTGGCAGTCC[A/T]
GTCAATATTTTTTTAAAAAAATAAGTAGGGCCCACCTGTCAGTTCCCACACCTATCTATCTCTCTCTCTCCCCAATCTCTCTCACTCTCTCTCTCTCTAT

Reverse complement sequence

ATAGAGAGAGAGAGAGTGAGAGAGATTGGGGAGAGAGAGAGATAGATAGGTGTGGGAACTGACAGGTGGGCCCTACTTATTTTTTTAAAAAAATATTGAC[T/A]
GGACTGCCACGTAGGACAAAACCACCATGGTTTGAGGCCGGGGCAGGGAGGGGGTTATTTGTTCGGCTTGCGTAGTTGGGGGTGAAGAATGTGTCCGGTT

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 87.40% 12.50% 0.04% 0.00% NA
All Indica  2759 96.20% 3.70% 0.04% 0.00% NA
All Japonica  1512 69.80% 30.20% 0.00% 0.00% NA
Aus  269 92.20% 7.80% 0.00% 0.00% NA
Indica I  595 89.40% 10.60% 0.00% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 97.70% 2.30% 0.00% 0.00% NA
Indica Intermediate  786 97.70% 2.20% 0.13% 0.00% NA
Temperate Japonica  767 93.50% 6.50% 0.00% 0.00% NA
Tropical Japonica  504 41.10% 58.90% 0.00% 0.00% NA
Japonica Intermediate  241 54.40% 45.60% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 86.70% 12.20% 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
vg1217338702 A -> T LOC_Os12g29250-LOC_Os12g29280 intergenic_region ; MODIFIER silent_mutation Average:52.355; most accessible tissue: Minghui63 young leaf, score: 65.92 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1217338702 5.89E-06 7.12E-08 mr1388 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
vg1217338702 NA 6.31E-07 mr1388 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
vg1217338702 NA 7.12E-09 mr1458 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
vg1217338702 NA 3.81E-06 mr1602 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
vg1217338702 NA 3.40E-06 mr1695 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
vg1217338702 1.55E-06 1.07E-12 mr1458_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