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Detailed information for vg1102590535:

Variant ID: vg1102590535 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 2590535
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GAAATTAAAGCAATGTCACGAAAATATTGAAAGTTTGTGTGTAGAATAATTTTTATGTGATGGAAAAGTTGGAAGTTTAAAGAAAAAGTTTGGAACTAAA[C/T]
TCGGCCCTGGTTGACAGCAAACTTTTAAAAATATAGTGAAGTTGAATTTTTCACCTTTTAATTTCTAGCTACGCCGTGTTTAGTTTCAAAATAATTCTTC

Reverse complement sequence

GAAGAATTATTTTGAAACTAAACACGGCGTAGCTAGAAATTAAAAGGTGAAAAATTCAACTTCACTATATTTTTAAAAGTTTGCTGTCAACCAGGGCCGA[G/A]
TTTAGTTCCAAACTTTTTCTTTAAACTTCCAACTTTTCCATCACATAAAAATTATTCTACACACAAACTTTCAATATTTTCGTGACATTGCTTTAATTTC

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 56.00% 6.60% 9.94% 27.47% NA
All Indica  2759 29.20% 11.10% 15.66% 44.00% NA
All Japonica  1512 99.20% 0.20% 0.00% 0.60% NA
Aus  269 65.80% 0.40% 11.15% 22.68% NA
Indica I  595 67.40% 14.30% 7.90% 10.42% NA
Indica II  465 9.50% 8.00% 6.45% 76.13% NA
Indica III  913 12.30% 6.90% 26.62% 54.22% NA
Indica Intermediate  786 31.80% 15.40% 14.25% 38.55% NA
Temperate Japonica  767 99.00% 0.30% 0.00% 0.78% NA
Tropical Japonica  504 99.60% 0.00% 0.00% 0.40% NA
Japonica Intermediate  241 99.20% 0.40% 0.00% 0.41% NA
VI/Aromatic  96 99.00% 0.00% 1.04% 0.00% NA
Intermediate  90 74.40% 2.20% 7.78% 15.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1102590535 C -> T LOC_Os11g05680-LOC_Os11g05690 intergenic_region ; MODIFIER silent_mutation Average:46.714; most accessible tissue: Callus, score: 90.843 N N N N
vg1102590535 C -> DEL N N silent_mutation Average:46.714; most accessible tissue: Callus, score: 90.843 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1102590535 4.52E-10 3.69E-12 mr1397 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