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Detailed information for vg1001281495:

Variant ID: vg1001281495 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 1281495
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GACTTGGGCATTTTGAAAATACTACTAGCACTACTAGTTGATTTGCTCACATATAAAAAGAAGTAGAGCACATGCAAGAGTTAAAAACTCCCCCTTAATG[T/C]
GACATGCTCCATTTTCACAAAGAAGAACCAAATGGCAATAAATCCAAAGCATAAGAGCAAATAGGAGCAAATATACAATATGCAAAAGAAGCAACCATGG

Reverse complement sequence

CCATGGTTGCTTCTTTTGCATATTGTATATTTGCTCCTATTTGCTCTTATGCTTTGGATTTATTGCCATTTGGTTCTTCTTTGTGAAAATGGAGCATGTC[A/G]
CATTAAGGGGGAGTTTTTAACTCTTGCATGTGCTCTACTTCTTTTTATATGTGAGCAAATCAACTAGTAGTGCTAGTAGTATTTTCAAAATGCCCAAGTC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 88.20% 3.70% 0.78% 7.34% NA
All Indica  2759 99.60% 0.30% 0.18% 0.00% NA
All Japonica  1512 67.20% 10.10% 1.79% 20.97% NA
Aus  269 99.60% 0.40% 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 99.10% 0.50% 0.33% 0.00% NA
Indica Intermediate  786 99.50% 0.30% 0.25% 0.00% NA
Temperate Japonica  767 87.60% 4.70% 0.52% 7.17% NA
Tropical Japonica  504 44.00% 17.90% 2.98% 35.12% NA
Japonica Intermediate  241 50.60% 10.80% 3.32% 35.27% NA
VI/Aromatic  96 55.20% 15.60% 5.21% 23.96% NA
Intermediate  90 91.10% 1.10% 0.00% 7.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1001281495 T -> C LOC_Os10g03070.1 intron_variant ; MODIFIER silent_mutation Average:23.349; most accessible tissue: Minghui63 flag leaf, score: 52.137 N N N N
vg1001281495 T -> DEL N N silent_mutation Average:23.349; most accessible tissue: Minghui63 flag leaf, score: 52.137 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1001281495 NA 1.24E-06 mr1886 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
vg1001281495 NA 1.52E-08 mr1057_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
vg1001281495 7.43E-07 NA mr1613_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
vg1001281495 8.21E-07 NA mr1913_2 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
vg1001281495 7.46E-06 NA mr1913_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