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

Detailed information for vg0114245822:

Variant ID: vg0114245822 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 14245822
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.75, G: 0.24, others allele: 0.00, population size: 72. )

Flanking Sequence (100 bp) in Reference Genome:


GGGCCACACATGGGCCGAGGTCCCAAACGAAGTTACAAGCCCATTGGCCCAATATAGGTGACGCAGCACCTTACTTCTGTGATTGCGGCCAAACGAAACG[A/G]
AACTCCGAGATGAGGCTAGATCCTTTGGAAAGAGGACTTTGAGAGCTTTCCATCAAGTACTCACGGGCCCAAAACGGAGCACGTATGTAGATTTGGCGGC

Reverse complement sequence

GCCGCCAAATCTACATACGTGCTCCGTTTTGGGCCCGTGAGTACTTGATGGAAAGCTCTCAAAGTCCTCTTTCCAAAGGATCTAGCCTCATCTCGGAGTT[T/C]
CGTTTCGTTTGGCCGCAATCACAGAAGTAAGGTGCTGCGTCACCTATATTGGGCCAATGGGCTTGTAACTTCGTTTGGGACCTCGGCCCATGTGTGGCCC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 35.40% 30.80% 0.78% 33.01% NA
All Indica  2759 3.50% 46.10% 1.09% 49.33% NA
All Japonica  1512 97.30% 2.60% 0.00% 0.13% NA
Aus  269 2.60% 32.30% 1.49% 63.57% NA
Indica I  595 4.20% 41.50% 1.34% 52.94% NA
Indica II  465 5.40% 23.40% 1.72% 69.46% NA
Indica III  913 1.10% 62.30% 0.55% 36.04% NA
Indica Intermediate  786 4.60% 44.10% 1.15% 50.13% NA
Temperate Japonica  767 98.60% 1.40% 0.00% 0.00% NA
Tropical Japonica  504 94.80% 5.00% 0.00% 0.20% NA
Japonica Intermediate  241 98.30% 1.20% 0.00% 0.41% NA
VI/Aromatic  96 53.10% 44.80% 0.00% 2.08% NA
Intermediate  90 52.20% 17.80% 3.33% 26.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0114245822 A -> G LOC_Os01g25210.1 synonymous_variant ; p.Phe97Phe; LOW synonymous_codon Average:34.229; most accessible tissue: Zhenshan97 panicle, score: 65.386 N N N N
vg0114245822 A -> DEL LOC_Os01g25210.1 N frameshift_variant Average:34.229; most accessible tissue: Zhenshan97 panicle, score: 65.386 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0114245822 NA 1.79E-06 mr1064 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
vg0114245822 NA 5.63E-07 mr1193 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
vg0114245822 5.56E-06 1.86E-06 mr1206 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
vg0114245822 NA 4.73E-06 mr1289 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
vg0114245822 7.06E-06 5.24E-07 mr1505 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
vg0114245822 NA 1.45E-08 mr1514 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
vg0114245822 NA 6.61E-06 mr1534 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
vg0114245822 NA 2.73E-07 mr1637 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
vg0114245822 NA 8.12E-06 mr1669 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
vg0114245822 NA 7.67E-06 mr1671 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
vg0114245822 8.55E-06 8.55E-06 mr1736 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
vg0114245822 NA 3.83E-06 mr1519_2 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