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Detailed information for vg0714218412:

Variant ID: vg0714218412 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 14218412
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: 31. )

Flanking Sequence (100 bp) in Reference Genome:


ATTTTGAAGTAAATTGGCTACCTCTATCTGACACGATCTTCTTAGGAACACCATGCAAACACACAATCCTGGCCATATATAATTCCGCTAAACGACTTCC[G/A]
GAATAGGTGGTCCTTACCGGGATGAAATGAGCCACTTTGGTAAGTCTGTCGACTATCACCCAAATAGAGTCATGGCCCAATGATGTTCTGGGTAGACCGG

Reverse complement sequence

CCGGTCTACCCAGAACATCATTGGGCCATGACTCTATTTGGGTGATAGTCGACAGACTTACCAAAGTGGCTCATTTCATCCCGGTAAGGACCACCTATTC[C/T]
GGAAGTCGTTTAGCGGAATTATATATGGCCAGGATTGTGTGTTTGCATGGTGTTCCTAAGAAGATCGTGTCAGATAGAGGTAGCCAATTTACTTCAAAAT

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 65.40% 10.60% 5.29% 18.75% NA
All Indica  2759 52.20% 17.50% 7.68% 22.58% NA
All Japonica  1512 84.30% 0.30% 1.39% 13.96% NA
Aus  269 84.40% 0.70% 1.86% 13.01% NA
Indica I  595 68.40% 2.40% 6.72% 22.52% NA
Indica II  465 42.40% 28.80% 8.60% 20.22% NA
Indica III  913 44.70% 22.00% 8.21% 25.08% NA
Indica Intermediate  786 54.50% 17.20% 7.25% 21.12% NA
Temperate Japonica  767 87.90% 0.30% 0.39% 11.47% NA
Tropical Japonica  504 83.70% 0.00% 2.38% 13.89% NA
Japonica Intermediate  241 74.30% 1.20% 2.49% 21.99% NA
VI/Aromatic  96 90.60% 1.00% 5.21% 3.12% NA
Intermediate  90 67.80% 8.90% 7.78% 15.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0714218412 G -> DEL LOC_Os07g24970.1 N frameshift_variant Average:7.947; most accessible tissue: Callus, score: 15.543 N N N N
vg0714218412 G -> A LOC_Os07g24970.1 synonymous_variant ; p.Ser172Ser; LOW synonymous_codon Average:7.947; most accessible tissue: Callus, score: 15.543 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0714218412 NA 5.10E-06 mr1308 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
vg0714218412 NA 7.35E-06 mr1603 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
vg0714218412 1.94E-06 NA mr1308_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
vg0714218412 2.73E-06 4.10E-07 mr1308_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
vg0714218412 NA 6.96E-06 mr1603_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
vg0714218412 8.18E-06 8.18E-06 mr1853_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