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Detailed information for vg0904129442:

Variant ID: vg0904129442 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 4129442
Reference Allele: CAlternative Allele: A
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, A: 0.03, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:


TAGTAGCAAAAGCAAGCAATATGCGAATCGACTCAAGTCTAGCTACCGGCGCAAAAGTTTCACCGAAATCTAATCCTTCGATTTGGGTGAACCCTTGCGC[C/A]
ACTAACCTCACCTTGTTCCTTATTATGACCCCGGCCTCGTCTTGCTTGTTGCGGAAGATCCACTTTGTGCCAATCACATTTTGCCGAGGTCGCTCCACCA

Reverse complement sequence

TGGTGGAGCGACCTCGGCAAAATGTGATTGGCACAAAGTGGATCTTCCGCAACAAGCAAGACGAGGCCGGGGTCATAATAAGGAACAAGGTGAGGTTAGT[G/T]
GCGCAAGGGTTCACCCAAATCGAAGGATTAGATTTCGGTGAAACTTTTGCGCCGGTAGCTAGACTTGAGTCGATTCGCATATTGCTTGCTTTTGCTACTA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 38.20% 34.60% 8.27% 18.92% NA
All Indica  2759 54.00% 7.10% 13.27% 25.70% NA
All Japonica  1512 1.00% 91.20% 0.73% 7.08% NA
Aus  269 99.30% 0.40% 0.00% 0.37% NA
Indica I  595 80.70% 9.20% 2.02% 8.07% NA
Indica II  465 54.80% 11.80% 4.52% 28.82% NA
Indica III  913 27.50% 2.50% 28.59% 41.40% NA
Indica Intermediate  786 64.00% 7.90% 9.16% 18.96% NA
Temperate Japonica  767 0.80% 86.40% 1.30% 11.47% NA
Tropical Japonica  504 1.20% 97.00% 0.00% 1.79% NA
Japonica Intermediate  241 1.20% 94.20% 0.41% 4.15% NA
VI/Aromatic  96 10.40% 14.60% 8.33% 66.67% NA
Intermediate  90 25.60% 53.30% 6.67% 14.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0904129442 C -> DEL LOC_Os09g08020.1 N frameshift_variant Average:20.203; most accessible tissue: Zhenshan97 flower, score: 47.586 N N N N
vg0904129442 C -> A LOC_Os09g08020.1 synonymous_variant ; p.Val1234Val; LOW synonymous_codon Average:20.203; most accessible tissue: Zhenshan97 flower, score: 47.586 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0904129442 NA 3.23E-06 mr1186_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
vg0904129442 NA 8.18E-06 mr1355_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
vg0904129442 NA 9.16E-07 mr1371_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
vg0904129442 8.78E-06 7.85E-07 mr1371_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
vg0904129442 NA 3.13E-09 mr1478_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
vg0904129442 NA 9.93E-08 mr1508_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
vg0904129442 NA 3.46E-06 mr1647_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
vg0904129442 NA 1.09E-08 mr1660_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
vg0904129442 NA 1.55E-11 mr1756_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
vg0904129442 1.06E-06 1.18E-07 mr1756_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
vg0904129442 NA 2.11E-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