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Search for Variation information by Variation ID:

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

Detailed information for vg0507142279:

Variant ID: vg0507142279 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 7142279
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: 0.25, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:


CATGCATGGATTGAGTCCTGAAAAGGCAATTGTATCTATTAATTAGGGTATTTCTTGTAATTTCCTTAGAGATAAGTTTGGGCAAAAGTCTGCCGCAAAG[A/G]
CTTATGGTATCTTAGAGTTTGTTAGAGATGAGAGTCGTGTCCGACATGGACATATTTTGTAATCTCGGGTATAAATAGACCCCGAGCCCCATGTAATACA

Reverse complement sequence

TGTATTACATGGGGCTCGGGGTCTATTTATACCCGAGATTACAAAATATGTCCATGTCGGACACGACTCTCATCTCTAACAAACTCTAAGATACCATAAG[T/C]
CTTTGCGGCAGACTTTTGCCCAAACTTATCTCTAAGGAAATTACAAGAAATACCCTAATTAATAGATACAATTGCCTTTTCAGGACTCAATCCATGCATG

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 58.80% 40.10% 0.25% 0.80% NA
All Indica  2759 40.30% 58.20% 0.36% 1.12% NA
All Japonica  1512 95.80% 3.90% 0.00% 0.26% NA
Aus  269 22.70% 76.60% 0.37% 0.37% NA
Indica I  595 18.20% 81.30% 0.34% 0.17% NA
Indica II  465 74.00% 24.90% 0.00% 1.08% NA
Indica III  913 40.60% 57.50% 0.44% 1.42% NA
Indica Intermediate  786 36.90% 61.10% 0.51% 1.53% NA
Temperate Japonica  767 99.50% 0.50% 0.00% 0.00% NA
Tropical Japonica  504 95.20% 4.20% 0.00% 0.60% NA
Japonica Intermediate  241 85.50% 14.10% 0.00% 0.41% NA
VI/Aromatic  96 97.90% 1.00% 1.04% 0.00% NA
Intermediate  90 71.10% 26.70% 0.00% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0507142279 A -> DEL LOC_Os05g12420.1 N frameshift_variant Average:27.83; most accessible tissue: Zhenshan97 flag leaf, score: 37.1 N N N N
vg0507142279 A -> G LOC_Os05g12420.1 missense_variant ; p.Thr243Ala; MODERATE nonsynonymous_codon ; T243A Average:27.83; most accessible tissue: Zhenshan97 flag leaf, score: 37.1 unknown unknown DELETERIOUS 0.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0507142279 NA 8.32E-09 mr1050 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
vg0507142279 NA 2.06E-11 mr1195 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
vg0507142279 1.23E-07 2.44E-10 mr1195 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
vg0507142279 NA 7.76E-12 mr1272 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
vg0507142279 6.00E-07 NA mr1531 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
vg0507142279 6.74E-08 8.50E-12 mr1531 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
vg0507142279 1.14E-27 7.75E-30 mr1593 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
vg0507142279 1.32E-42 5.74E-75 mr1593 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
vg0507142279 NA 4.56E-12 mr1904 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
vg0507142279 2.41E-10 8.39E-33 mr1195_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
vg0507142279 2.35E-12 8.26E-24 mr1195_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
vg0507142279 NA 1.52E-09 mr1378_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
vg0507142279 NA 1.17E-10 mr1482_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
vg0507142279 NA 1.29E-07 mr1482_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
vg0507142279 5.39E-09 NA mr1531_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
vg0507142279 6.08E-10 1.05E-14 mr1531_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
vg0507142279 2.64E-30 6.92E-38 mr1593_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
vg0507142279 1.53E-49 4.87E-93 mr1593_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
vg0507142279 NA 1.15E-09 mr1739_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
vg0507142279 NA 1.65E-08 mr1748_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
vg0507142279 8.62E-07 3.25E-11 mr1807_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
vg0507142279 NA 1.34E-06 mr1977_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