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Detailed information for vg1005170915:

Variant ID: vg1005170915 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 5170915
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 43. )

Flanking Sequence (100 bp) in Reference Genome:


GTCGACTCGCACCCTCGCGTATCTGATCGCTAAAGACCAGGGAGCCATCCACTGGGTTGAACGTTCCACCGTGAGCATAGTAACAGAACTTCGATCGATC[C/T]
GGCCATTAAGCGGTGGCCGGTTCGATACCCCTCTCAAGCAAGCTTGCCTCCATCTCCTCCCACTTTGGCATCGTGACGCTATAGCCGCCTGACCCCAAGT

Reverse complement sequence

ACTTGGGGTCAGGCGGCTATAGCGTCACGATGCCAAAGTGGGAGGAGATGGAGGCAAGCTTGCTTGAGAGGGGTATCGAACCGGCCACCGCTTAATGGCC[G/A]
GATCGATCGAAGTTCTGTTACTATGCTCACGGTGGAACGTTCAACCCAGTGGATGGCTCCCTGGTCTTTAGCGATCAGATACGCGAGGGTGCGAGTCGAC

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 57.40% 40.60% 0.25% 1.67% NA
All Indica  2759 43.70% 55.90% 0.29% 0.11% NA
All Japonica  1512 91.50% 5.00% 0.26% 3.17% NA
Aus  269 4.50% 95.20% 0.00% 0.37% NA
Indica I  595 25.70% 73.90% 0.34% 0.00% NA
Indica II  465 52.70% 47.10% 0.22% 0.00% NA
Indica III  913 54.80% 44.90% 0.22% 0.11% NA
Indica Intermediate  786 39.30% 60.10% 0.38% 0.25% NA
Temperate Japonica  767 93.50% 1.70% 0.52% 4.30% NA
Tropical Japonica  504 89.50% 10.10% 0.00% 0.40% NA
Japonica Intermediate  241 89.60% 5.00% 0.00% 5.39% NA
VI/Aromatic  96 52.10% 24.00% 0.00% 23.96% NA
Intermediate  90 67.80% 27.80% 0.00% 4.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1005170915 C -> T LOC_Os10g09570-LOC_Os10g09590 intergenic_region ; MODIFIER silent_mutation Average:40.465; most accessible tissue: Minghui63 young leaf, score: 75.937 N N N N
vg1005170915 C -> DEL N N silent_mutation Average:40.465; most accessible tissue: Minghui63 young leaf, score: 75.937 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1005170915 NA 2.36E-07 mr1245 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
vg1005170915 NA 9.39E-06 mr1373 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
vg1005170915 NA 3.34E-06 mr1424 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
vg1005170915 NA 2.62E-07 mr1445 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
vg1005170915 NA 2.43E-07 mr1574 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
vg1005170915 NA 2.70E-06 mr1681 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
vg1005170915 NA 1.55E-10 mr1730 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
vg1005170915 NA 1.03E-12 mr1853 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
vg1005170915 NA 3.21E-12 mr1866 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
vg1005170915 NA 2.52E-06 mr1881 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
vg1005170915 NA 2.87E-09 mr1986 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