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Detailed information for vg0119647380:

Variant ID: vg0119647380 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 19647380
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:


TTTTGATGAACAACGTGAATCTAAAAGCATAGAACATGTTTTTGGTCTTAGGACGATAATCCAATTACCGGCCATAGTACCTCCTAAGCGTCTTGCCAAA[C/T]
ACTCGGGAAGTATATCTTCAAGTATTTCCCGTTGATCGCTCGCTGAAAACGCTCCCCTTGAAGTGTCTCAAAAAAGTATGCGTTCCCTCGAACAATGCCG

Reverse complement sequence

CGGCATTGTTCGAGGGAACGCATACTTTTTTGAGACACTTCAAGGGGAGCGTTTTCAGCGAGCGATCAACGGGAAATACTTGAAGATATACTTCCCGAGT[G/A]
TTTGGCAAGACGCTTAGGAGGTACTATGGCCGGTAATTGGATTATCGTCCTAAGACCAAAAACATGTTCTATGCTTTTAGATTCACGTTGTTCATCAAAA

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 83.60% 15.60% 0.72% 0.15% NA
All Indica  2759 72.20% 26.40% 1.20% 0.25% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 98.80% 1.20% 0.00% 0.00% NA
Indica II  465 95.90% 3.90% 0.22% 0.00% NA
Indica III  913 38.00% 57.90% 3.40% 0.66% NA
Indica Intermediate  786 77.60% 22.10% 0.13% 0.13% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 93.30% 5.60% 1.11% 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
vg0119647380 C -> T LOC_Os01g35504.1 intron_variant ; MODIFIER silent_mutation Average:43.998; most accessible tissue: Minghui63 flag leaf, score: 67.099 N N N N
vg0119647380 C -> DEL N N silent_mutation Average:43.998; most accessible tissue: Minghui63 flag leaf, score: 67.099 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0119647380 NA 4.50E-06 mr1973 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
vg0119647380 2.19E-06 NA mr1224_2 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
vg0119647380 NA 2.23E-07 mr1973_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