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Detailed information for vg1202275914:

Variant ID: vg1202275914 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 2275914
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:


TTGCTGGCGGCAGCAAGATGACGACACACGGCTTGGGAGGGACAGAGCGGCACGGAATGAAACAATTCACGTCCTTGGTGGCATGTTTTGAAAGTGTTGC[G/A]
AATTGAGTGGCACATCCTGAAGGTGGTGCAGCAAATCGAATGGCATCTTCTAAAAATTCTCTCCTAAACCATTTGTAATATGTGATAGTAGAAATGCCGG

Reverse complement sequence

CCGGCATTTCTACTATCACATATTACAAATGGTTTAGGAGAGAATTTTTAGAAGATGCCATTCGATTTGCTGCACCACCTTCAGGATGTGCCACTCAATT[C/T]
GCAACACTTTCAAAACATGCCACCAAGGACGTGAATTGTTTCATTCCGTGCCGCTCTGTCCCTCCCAAGCCGTGTGTCGTCATCTTGCTGCCGCCAGCAA

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 91.60% 8.40% 0.00% 0.00% NA
All Indica  2759 93.80% 6.20% 0.00% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 19.00% 81.00% 0.00% 0.00% NA
Indica I  595 99.20% 0.80% 0.00% 0.00% NA
Indica II  465 98.10% 1.90% 0.00% 0.00% NA
Indica III  913 90.60% 9.40% 0.00% 0.00% NA
Indica Intermediate  786 91.10% 8.90% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 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
vg1202275914 G -> A LOC_Os12g05144.1 upstream_gene_variant ; 2544.0bp to feature; MODIFIER silent_mutation Average:41.124; most accessible tissue: Minghui63 panicle, score: 64.459 N N N N
vg1202275914 G -> A LOC_Os12g05151.1 upstream_gene_variant ; 2030.0bp to feature; MODIFIER silent_mutation Average:41.124; most accessible tissue: Minghui63 panicle, score: 64.459 N N N N
vg1202275914 G -> A LOC_Os12g05151-LOC_Os12g05160 intergenic_region ; MODIFIER silent_mutation Average:41.124; most accessible tissue: Minghui63 panicle, score: 64.459 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1202275914 NA 6.95E-07 mr1764 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
vg1202275914 3.16E-06 6.93E-25 mr1099_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
vg1202275914 NA 1.99E-14 mr1936_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