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Detailed information for vg0219416709:

Variant ID: vg0219416709 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 19416709
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:


CTAATTATATAGTTTTTAAAAGTCACACCAGCTGCTACCCCTTACTTCTGTCATATCCTTCTTTATTTTCTTGCTCGGTCTACCACTATTTCTATTCATT[C/T]
TCCTTGAAACCTTTAAAATTTGGATCTTATATAGTTTTTTGAGTTTATTATCTCGTTGGGTTTCGTTTTTATAATTTCTAGAAGTCCCGTCAAACGAATT

Reverse complement sequence

AATTCGTTTGACGGGACTTCTAGAAATTATAAAAACGAAACCCAACGAGATAATAAACTCAAAAAACTATATAAGATCCAAATTTTAAAGGTTTCAAGGA[G/A]
AATGAATAGAAATAGTGGTAGACCGAGCAAGAAAATAAAGAAGGATATGACAGAAGTAAGGGGTAGCAGCTGGTGTGACTTTTAAAAACTATATAATTAG

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 88.60% 9.20% 2.18% 0.00% NA
All Indica  2759 96.00% 2.50% 1.41% 0.00% NA
All Japonica  1512 76.10% 20.20% 3.77% 0.00% NA
Aus  269 82.20% 17.10% 0.74% 0.00% NA
Indica I  595 92.80% 3.20% 4.03% 0.00% NA
Indica II  465 96.10% 3.20% 0.65% 0.00% NA
Indica III  913 99.70% 0.20% 0.11% 0.00% NA
Indica Intermediate  786 94.30% 4.30% 1.40% 0.00% NA
Temperate Japonica  767 96.00% 0.50% 3.52% 0.00% NA
Tropical Japonica  504 38.30% 56.50% 5.16% 0.00% NA
Japonica Intermediate  241 91.70% 6.60% 1.66% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 80.00% 14.40% 5.56% 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
vg0219416709 C -> T LOC_Os02g32690.1 intron_variant ; MODIFIER silent_mutation Average:52.65; most accessible tissue: Minghui63 flag leaf, score: 97.555 N N N N
vg0219416709 C -> T LOC_Os02g32690.2 intron_variant ; MODIFIER silent_mutation Average:52.65; most accessible tissue: Minghui63 flag leaf, score: 97.555 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0219416709 NA 5.43E-06 mr1076 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
vg0219416709 NA 2.18E-07 mr1082 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
vg0219416709 NA 2.47E-07 mr1083 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
vg0219416709 1.55E-06 NA mr1136 Jap_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
vg0219416709 NA 1.78E-06 mr1226 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
vg0219416709 NA 9.38E-08 mr1551 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
vg0219416709 NA 1.26E-06 mr1082_2 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
vg0219416709 NA 2.35E-06 mr1423_2 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