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Detailed information for vg1005421909:

Variant ID: vg1005421909 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 5421909
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.00, others allele: 0.00, population size: 322. )

Flanking Sequence (100 bp) in Reference Genome:


TTCCAAGAGCAAGCACCCGCAACCCTAAACAGTAGACCACCAAGCCCTTAGCAGACCAGCACAGCCAAGCCGCCACTAATCCTAGGAGCAACAAGTGATA[C/T]
CTACAGAAGGTATGGGTTTCAAGGGCACCGATAAAGATTCTATTGTTTCGCTAGCAACTGCTTCAAGGCTACAGAATCAGCATTAGTAGGGCAATCAATG

Reverse complement sequence

CATTGATTGCCCTACTAATGCTGATTCTGTAGCCTTGAAGCAGTTGCTAGCGAAACAATAGAATCTTTATCGGTGCCCTTGAAACCCATACCTTCTGTAG[G/A]
TATCACTTGTTGCTCCTAGGATTAGTGGCGGCTTGGCTGTGCTGGTCTGCTAAGGGCTTGGTGGTCTACTGTTTAGGGTTGCGGGTGCTTGCTCTTGGAA

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 68.00% 9.40% 1.97% 20.69% NA
All Indica  2759 55.30% 13.70% 3.19% 27.84% NA
All Japonica  1512 96.20% 0.20% 0.20% 3.44% NA
Aus  269 20.40% 22.70% 0.37% 56.51% NA
Indica I  595 38.20% 36.00% 5.71% 20.17% NA
Indica II  465 82.60% 3.20% 2.80% 11.40% NA
Indica III  913 48.40% 4.70% 1.97% 44.91% NA
Indica Intermediate  786 60.20% 13.40% 2.93% 23.54% NA
Temperate Japonica  767 93.40% 0.30% 0.26% 6.13% NA
Tropical Japonica  504 99.20% 0.00% 0.00% 0.79% NA
Japonica Intermediate  241 98.80% 0.40% 0.41% 0.41% NA
VI/Aromatic  96 99.00% 0.00% 0.00% 1.04% NA
Intermediate  90 91.10% 2.20% 1.11% 5.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1005421909 C -> T LOC_Os10g09990-LOC_Os10g10000 intergenic_region ; MODIFIER silent_mutation Average:18.412; most accessible tissue: Minghui63 panicle, score: 38.588 N N N N
vg1005421909 C -> DEL N N silent_mutation Average:18.412; most accessible tissue: Minghui63 panicle, score: 38.588 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1005421909 NA 5.93E-06 mr1231 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
vg1005421909 6.06E-06 NA mr1458 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
vg1005421909 1.86E-06 3.73E-08 mr1547 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
vg1005421909 NA 7.60E-07 mr1547 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
vg1005421909 NA 2.51E-07 mr1557 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
vg1005421909 2.13E-07 3.39E-18 mr1598 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
vg1005421909 3.62E-06 1.98E-09 mr1598 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
vg1005421909 5.85E-06 NA mr1620 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
vg1005421909 2.66E-06 NA mr1676 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
vg1005421909 9.38E-06 7.19E-08 mr1748 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
vg1005421909 3.61E-06 3.61E-06 mr1748 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
vg1005421909 NA 4.66E-07 mr1785 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