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Detailed information for vg0915258271:

Variant ID: vg0915258271 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 15258271
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTTTTTTTCACCCCTAGAAGCCAATTATCAAAAATATGTGATATACCATGAGGAAGGTAAAGAACAAAAGAAAACTGAACTGCTCTCCATAAAAACTTTT[C/T]
ATAATGATACTCCACAAATAGATGTTGAATAGTCTCATTTTTCATACAGAAACAACATCTCAAGCTACCATTCCAATTTCTCGTGGCCAAATTATCTTTA

Reverse complement sequence

TAAAGATAATTTGGCCACGAGAAATTGGAATGGTAGCTTGAGATGTTGTTTCTGTATGAAAAATGAGACTATTCAACATCTATTTGTGGAGTATCATTAT[G/A]
AAAAGTTTTTATGGAGAGCAGTTCAGTTTTCTTTTGTTCTTTACCTTCCTCATGGTATATCACATATTTTTGATAATTGGCTTCTAGGGGTGAAAAAAAA

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 97.60% 2.00% 0.44% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 92.70% 6.00% 1.32% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 99.10% 0.80% 0.13% 0.00% NA
Tropical Japonica  504 84.50% 12.10% 3.37% 0.00% NA
Japonica Intermediate  241 89.60% 9.50% 0.83% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 95.60% 3.30% 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
vg0915258271 C -> T LOC_Os09g25460.1 upstream_gene_variant ; 1943.0bp to feature; MODIFIER silent_mutation Average:32.3; most accessible tissue: Minghui63 panicle, score: 53.77 N N N N
vg0915258271 C -> T LOC_Os09g25460-LOC_Os09g25470 intergenic_region ; MODIFIER silent_mutation Average:32.3; most accessible tissue: Minghui63 panicle, score: 53.77 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0915258271 NA 5.06E-06 mr1044 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
vg0915258271 NA 5.08E-07 mr1156 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
vg0915258271 NA 8.59E-07 mr1179 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
vg0915258271 NA 7.35E-08 mr1194 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
vg0915258271 NA 5.25E-10 mr1668 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
vg0915258271 NA 7.89E-07 mr1951 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