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Detailed information for vg0204058310:

Variant ID: vg0204058310 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 4058310
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: 94. )

Flanking Sequence (100 bp) in Reference Genome:


ACCCGTAGGATAGGTTCCTCGTCTGAGCTCCGGCCATCACCGACGGGCTCCCCAGCTGCGGCGGCCGCCGCGGCGACGGCCTCTCCAGCTTCGACGCCGC[C/T]
GCCGCGACGTCGTAGCCGCCGCCCTTGCTCCCCGTCGAGTCGCCGGACATGATCGGCTTCGTCTCGTAGACGTCGGCGGCGAGGGAGTCCATGACGTCGA

Reverse complement sequence

TCGACGTCATGGACTCCCTCGCCGCCGACGTCTACGAGACGAAGCCGATCATGTCCGGCGACTCGACGGGGAGCAAGGGCGGCGGCTACGACGTCGCGGC[G/A]
GCGGCGTCGAAGCTGGAGAGGCCGTCGCCGCGGCGGCCGCCGCAGCTGGGGAGCCCGTCGGTGATGGCCGGAGCTCAGACGAGGAACCTATCCTACGGGT

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 68.40% 31.50% 0.11% 0.00% NA
All Indica  2759 46.80% 53.10% 0.14% 0.00% NA
All Japonica  1512 99.80% 0.20% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 33.40% 66.60% 0.00% 0.00% NA
Indica II  465 41.10% 58.50% 0.43% 0.00% NA
Indica III  913 60.20% 39.60% 0.11% 0.00% NA
Indica Intermediate  786 44.70% 55.20% 0.13% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 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 76.70% 22.20% 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
vg0204058310 C -> T LOC_Os02g07770.1 synonymous_variant ; p.Ala322Ala; LOW synonymous_codon Average:60.529; most accessible tissue: Minghui63 panicle, score: 85.556 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0204058310 NA 9.62E-07 mr1561 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
vg0204058310 NA 2.72E-07 mr1826 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
vg0204058310 NA 5.43E-06 mr1826 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
vg0204058310 NA 6.34E-06 mr1929_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