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

Detailed information for vg1215652345:

Variant ID: vg1215652345 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 15652345
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: 81. )

Flanking Sequence (100 bp) in Reference Genome:


AATATTGTGATAATTAATATGACTCCTGGTTTGGAATGGTATATTCCTGGTATGGAGGTTTGATTTGTACAACCGGGGTTGGTTGTTCAGATGAGGTTGG[G/A]
CCTATGCAACACGGGTGTGTTGTATAGTGTTTATTTAATACTGATTAATTATCCAACTGTTTTATTATTCTCTAAAATGTTTATTAAATGCTATTTATGC

Reverse complement sequence

GCATAAATAGCATTTAATAAACATTTTAGAGAATAATAAAACAGTTGGATAATTAATCAGTATTAAATAAACACTATACAACACACCCGTGTTGCATAGG[C/T]
CCAACCTCATCTGAACAACCAACCCCGGTTGTACAAATCAAACCTCCATACCAGGAATATACCATTCCAAACCAGGAGTCATATTAATTATCACAATATT

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 82.20% 10.10% 6.28% 1.50% NA
All Indica  2759 85.90% 2.60% 9.17% 2.39% NA
All Japonica  1512 76.40% 20.70% 2.58% 0.33% NA
Aus  269 91.10% 8.60% 0.37% 0.00% NA
Indica I  595 83.40% 0.20% 14.45% 2.02% NA
Indica II  465 83.70% 9.70% 5.16% 1.51% NA
Indica III  913 87.80% 1.30% 7.45% 3.40% NA
Indica Intermediate  786 86.80% 1.70% 9.54% 2.04% NA
Temperate Japonica  767 94.00% 4.20% 1.56% 0.26% NA
Tropical Japonica  504 50.20% 45.20% 4.17% 0.40% NA
Japonica Intermediate  241 75.10% 22.00% 2.49% 0.41% NA
VI/Aromatic  96 42.70% 57.30% 0.00% 0.00% NA
Intermediate  90 81.10% 14.40% 4.44% 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
vg1215652345 G -> DEL N N silent_mutation Average:22.495; most accessible tissue: Minghui63 young leaf, score: 55.178 N N N N
vg1215652345 G -> A LOC_Os12g26710.1 intron_variant ; MODIFIER silent_mutation Average:22.495; most accessible tissue: Minghui63 young leaf, score: 55.178 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1215652345 NA 2.63E-09 mr1057_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
vg1215652345 1.34E-06 1.34E-06 mr1367_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
vg1215652345 2.69E-06 8.72E-11 mr1408_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
vg1215652345 NA 2.67E-06 mr1421_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
vg1215652345 NA 8.86E-07 mr1554_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
vg1215652345 1.37E-06 NA mr1730_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
vg1215652345 NA 2.23E-07 mr1730_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
vg1215652345 NA 4.03E-06 mr1852_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
vg1215652345 9.92E-08 NA mr1866_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
vg1215652345 NA 4.35E-06 mr1866_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
vg1215652345 NA 3.02E-06 mr1915_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