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Detailed information for vg0401160396:

Variant ID: vg0401160396 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 1160396
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCGAAAAGATTTGTCGATACAAAATTGTTACTAGAATAAATAATGAAAAAAATCCAAATGGCAATACAAACGAAATTTAATTACAAGTCAATATAGAAAT[C/A]
GAAATAGAATGATAGTCTTGCAATTTACACAGACGGTTGTGTGTTCTATGAGCTGATCCATGCCTTTGCATGTTCTCAAATTTCTATCATGGCCTAAACA

Reverse complement sequence

TGTTTAGGCCATGATAGAAATTTGAGAACATGCAAAGGCATGGATCAGCTCATAGAACACACAACCGTCTGTGTAAATTGCAAGACTATCATTCTATTTC[G/T]
ATTTCTATATTGACTTGTAATTAAATTTCGTTTGTATTGCCATTTGGATTTTTTTCATTATTTATTCTAGTAACAATTTTGTATCGACAAATCTTTTCGG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 88.70% 10.90% 0.44% 0.00% NA
All Indica  2759 86.00% 13.30% 0.76% 0.00% NA
All Japonica  1512 96.60% 3.40% 0.00% 0.00% NA
Aus  269 70.30% 29.70% 0.00% 0.00% NA
Indica I  595 85.20% 14.80% 0.00% 0.00% NA
Indica II  465 98.90% 1.10% 0.00% 0.00% NA
Indica III  913 78.60% 19.20% 2.19% 0.00% NA
Indica Intermediate  786 87.40% 12.50% 0.13% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 90.10% 9.90% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 93.80% 6.20% 0.00% 0.00% NA
Intermediate  90 88.90% 11.10% 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
vg0401160396 C -> A LOC_Os04g02920.1 upstream_gene_variant ; 250.0bp to feature; MODIFIER silent_mutation Average:41.864; most accessible tissue: Minghui63 root, score: 75.485 N N N N
vg0401160396 C -> A LOC_Os04g02910-LOC_Os04g02920 intergenic_region ; MODIFIER silent_mutation Average:41.864; most accessible tissue: Minghui63 root, score: 75.485 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0401160396 NA 4.37E-06 mr1086 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
vg0401160396 NA 1.86E-06 mr1107 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
vg0401160396 NA 7.62E-06 mr1210 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
vg0401160396 NA 5.61E-09 mr1213 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
vg0401160396 NA 9.14E-06 mr1246 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
vg0401160396 NA 2.93E-06 mr1337 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
vg0401160396 1.72E-06 1.72E-06 mr1381 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
vg0401160396 1.33E-06 NA mr1878 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
vg0401160396 NA 4.38E-07 mr1878 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