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Detailed information for vg1115833983:

Variant ID: vg1115833983 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 15833983
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCGTGAATCTTCTGAACTTCCAGTCCTAGAGGGCAGACTATCTTCTTAGCCTCATATGTTGTCTCGGGCAATTTGTTTCCCTCCGGAAGAATGTTCTTGA[C/T]
GAGTCTCAATTAATCGCCAAATGTCTTGTCACTAACACCATTTTTTGCCTTCCATTGCAAGAACTCCAGAGTGGTATCCAACTTTTTGTGCCCCTGCTCG

Reverse complement sequence

CGAGCAGGGGCACAAAAAGTTGGATACCACTCTGGAGTTCTTGCAATGGAAGGCAAAAAATGGTGTTAGTGACAAGACATTTGGCGATTAATTGAGACTC[G/A]
TCAAGAACATTCTTCCGGAGGGAAACAAATTGCCCGAGACAACATATGAGGCTAAGAAGATAGTCTGCCCTCTAGGACTGGAAGTTCAGAAGATTCACGC

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 86.50% 0.20% 5.82% 7.47% NA
All Indica  2759 78.40% 0.10% 9.39% 12.03% NA
All Japonica  1512 99.00% 0.30% 0.33% 0.40% NA
Aus  269 94.40% 0.00% 2.23% 3.35% NA
Indica I  595 60.20% 0.30% 16.97% 22.52% NA
Indica II  465 85.40% 0.00% 10.11% 4.52% NA
Indica III  913 84.10% 0.10% 5.15% 10.62% NA
Indica Intermediate  786 81.60% 0.10% 8.14% 10.18% NA
Temperate Japonica  767 99.00% 0.50% 0.39% 0.13% NA
Tropical Japonica  504 99.20% 0.00% 0.20% 0.60% NA
Japonica Intermediate  241 98.80% 0.00% 0.41% 0.83% NA
VI/Aromatic  96 99.00% 0.00% 1.04% 0.00% NA
Intermediate  90 88.90% 0.00% 4.44% 6.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1115833983 C -> T LOC_Os11g27520.1 intron_variant ; MODIFIER silent_mutation Average:14.858; most accessible tissue: Callus, score: 25.527 N N N N
vg1115833983 C -> DEL N N silent_mutation Average:14.858; most accessible tissue: Callus, score: 25.527 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1115833983 NA 2.69E-06 mr1042 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
vg1115833983 1.16E-06 1.54E-06 mr1707 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
vg1115833983 NA 2.50E-06 mr1860_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
vg1115833983 7.17E-06 1.16E-07 mr1864_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