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Detailed information for vg0409247981:

Variant ID: vg0409247981 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 9247981
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTCTATTATCAATTTGTTATTGTGTGCCTCGGCTGATTCCTGGACGAGGGTTCACACACATGTAAGTGTTTGGAATTTTGGATGGAAATTCCGGGCGTGA[A/C]
AAGTTGGTATCAGAGCCCCTTTGACCCTAGGTTATGCCAAATGGTTACCCATAGAAGCCCTCTAAAAATATTGGAAAAGTAGAACTGTTCTCCTCTCCTT

Reverse complement sequence

AAGGAGAGGAGAACAGTTCTACTTTTCCAATATTTTTAGAGGGCTTCTATGGGTAACCATTTGGCATAACCTAGGGTCAAAGGGGCTCTGATACCAACTT[T/G]
TCACGCCCGGAATTTCCATCCAAAATTCCAAACACTTACATGTGTGTGAACCCTCGTCCAGGAATCAGCCGAGGCACACAATAACAAATTGATAATAGAG

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 21.20% 0.20% 31.63% 47.02% NA
All Indica  2759 2.00% 0.30% 45.99% 51.76% NA
All Japonica  1512 61.00% 0.10% 0.46% 38.36% NA
Aus  269 0.40% 0.00% 66.54% 33.09% NA
Indica I  595 0.70% 0.00% 27.06% 72.27% NA
Indica II  465 2.20% 0.00% 30.75% 67.10% NA
Indica III  913 1.60% 0.50% 69.33% 28.48% NA
Indica Intermediate  786 3.30% 0.30% 42.24% 54.20% NA
Temperate Japonica  767 96.00% 0.00% 0.00% 4.04% NA
Tropical Japonica  504 4.20% 0.00% 1.39% 94.44% NA
Japonica Intermediate  241 68.90% 0.80% 0.00% 30.29% NA
VI/Aromatic  96 2.10% 0.00% 16.67% 81.25% NA
Intermediate  90 21.10% 0.00% 26.67% 52.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0409247981 A -> C LOC_Os04g16900.1 downstream_gene_variant ; 3243.0bp to feature; MODIFIER silent_mutation Average:7.471; most accessible tissue: Minghui63 panicle, score: 20.733 N N N N
vg0409247981 A -> C LOC_Os04g16910.1 intron_variant ; MODIFIER silent_mutation Average:7.471; most accessible tissue: Minghui63 panicle, score: 20.733 N N N N
vg0409247981 A -> DEL N N silent_mutation Average:7.471; most accessible tissue: Minghui63 panicle, score: 20.733 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0409247981 NA 1.14E-07 mr1194 Jap_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
vg0409247981 NA 4.00E-07 mr1206 Jap_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
vg0409247981 NA 9.54E-11 mr1454 Jap_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
vg0409247981 2.62E-06 2.63E-36 mr1789 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
vg0409247981 NA 1.30E-39 mr1926 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
vg0409247981 NA 2.51E-12 mr1248_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
vg0409247981 NA 1.38E-07 mr1399_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
vg0409247981 NA 2.02E-28 mr1789_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