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Detailed information for vg0405536257:

Variant ID: vg0405536257 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 5536257
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AACATGTGTTCCCGGCCACCATGAGTCAATCTATGCCCTCAGCCGCATTAGCAGCAGCGGCGCCACCGGTTTCCCTCACCGCGACTAAGGAGGATGAGGC[C/T]
GACATGGACAAATCTGAGATGAAACCAGAGGAGACATTCCAAGAGTTGTGTGCCAAGATGATTGCCATGCTCAACAACATGCTCGTGACATGCTGCGACA

Reverse complement sequence

TGTCGCAGCATGTCACGAGCATGTTGTTGAGCATGGCAATCATCTTGGCACACAACTCTTGGAATGTCTCCTCTGGTTTCATCTCAGATTTGTCCATGTC[G/A]
GCCTCATCCTCCTTAGTCGCGGTGAGGGAAACCGGTGGCGCCGCTGCTGCTAATGCGGCTGAGGGCATAGATTGACTCATGGTGGCCGGGAACACATGTT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 33.70% 5.40% 3.66% 57.30% NA
All Indica  2759 14.70% 9.00% 4.86% 71.51% NA
All Japonica  1512 67.40% 0.10% 0.46% 32.01% NA
Aus  269 51.30% 0.00% 6.69% 42.01% NA
Indica I  595 5.20% 4.20% 3.03% 87.56% NA
Indica II  465 19.40% 16.10% 6.88% 57.63% NA
Indica III  913 15.40% 13.50% 5.37% 65.72% NA
Indica Intermediate  786 18.20% 3.10% 4.45% 74.30% NA
Temperate Japonica  767 66.00% 0.10% 0.52% 33.38% NA
Tropical Japonica  504 63.50% 0.00% 0.20% 36.31% NA
Japonica Intermediate  241 80.10% 0.40% 0.83% 18.67% NA
VI/Aromatic  96 0.00% 0.00% 9.38% 90.62% NA
Intermediate  90 33.30% 4.40% 5.56% 56.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0405536257 C -> DEL LOC_Os04g10250.1 N frameshift_variant Average:49.642; most accessible tissue: Minghui63 flag leaf, score: 87.98 N N N N
vg0405536257 C -> T LOC_Os04g10250.1 synonymous_variant ; p.Ala167Ala; LOW synonymous_codon Average:49.642; most accessible tissue: Minghui63 flag leaf, score: 87.98 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0405536257 NA 1.65E-17 mr1035 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
vg0405536257 7.41E-08 7.70E-10 mr1035 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
vg0405536257 1.03E-06 2.92E-18 mr1062 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
vg0405536257 1.04E-07 1.98E-08 mr1062 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
vg0405536257 6.25E-06 NA mr1525 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
vg0405536257 2.24E-08 6.99E-09 mr1525 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
vg0405536257 NA 1.64E-14 mr1626 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
vg0405536257 3.57E-06 1.02E-07 mr1626 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
vg0405536257 NA 4.27E-06 mr1631 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
vg0405536257 NA 4.42E-08 mr1806 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
vg0405536257 NA 2.00E-14 mr1035_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
vg0405536257 4.58E-06 4.58E-06 mr1035_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
vg0405536257 NA 3.83E-19 mr1062_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
vg0405536257 1.08E-07 5.14E-09 mr1062_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
vg0405536257 8.30E-07 3.47E-08 mr1525_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
vg0405536257 4.48E-06 7.01E-07 mr1631_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