\

Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg1105605348:

Variant ID: vg1105605348 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 5605348
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.92, T: 0.08, others allele: 0.00, population size: 100. )

Flanking Sequence (100 bp) in Reference Genome:


TCTTCGCAGACAAAGCTTGCTAGCTCTACACACTCACAGAAGTTCAGAAATGGCTGCGAAGTTCCCAATTCTTCTTGGTGTCATATTGGCCACTCTCCTT[C/T]
TCGTCTCCCACGATGTAGCGCATGCAGCAGGTACGGTGGTTTTCAAACTGAGGGTGTGTTTGTTTCTCTGGGTGTAAAATTTTTTGACGTATAAGGGACA

Reverse complement sequence

TGTCCCTTATACGTCAAAAAATTTTACACCCAGAGAAACAAACACACCCTCAGTTTGAAAACCACCGTACCTGCTGCATGCGCTACATCGTGGGAGACGA[G/A]
AAGGAGAGTGGCCAATATGACACCAAGAAGAATTGGGAACTTCGCAGCCATTTCTGAACTTCTGTGAGTGTGTAGAGCTAGCAAGCTTTGTCTGCGAAGA

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 46.80% 43.30% 0.25% 9.65% NA
All Indica  2759 66.20% 27.90% 0.22% 5.65% NA
All Japonica  1512 5.60% 81.10% 0.00% 13.36% NA
Aus  269 91.40% 4.50% 0.74% 3.35% NA
Indica I  595 28.60% 58.00% 0.50% 12.94% NA
Indica II  465 89.00% 9.90% 0.22% 0.86% NA
Indica III  913 78.60% 16.30% 0.00% 5.04% NA
Indica Intermediate  786 66.70% 29.40% 0.25% 3.69% NA
Temperate Japonica  767 2.30% 88.70% 0.00% 9.00% NA
Tropical Japonica  504 9.90% 78.80% 0.00% 11.31% NA
Japonica Intermediate  241 6.60% 61.80% 0.00% 31.54% NA
VI/Aromatic  96 12.50% 0.00% 3.12% 84.38% NA
Intermediate  90 47.80% 42.20% 1.11% 8.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1105605348 C -> T LOC_Os11g10320.1 missense_variant ; p.Leu18Phe; MODERATE nonsynonymous_codon ; L18F Average:74.147; most accessible tissue: Zhenshan97 panicle, score: 86.432 unknown unknown DELETERIOUS 0.00
vg1105605348 C -> DEL LOC_Os11g10320.1 N frameshift_variant Average:74.147; most accessible tissue: Zhenshan97 panicle, score: 86.432 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1105605348 2.43E-06 NA mr1003 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
vg1105605348 NA 3.28E-06 mr1004 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
vg1105605348 NA 2.87E-07 mr1904 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
vg1105605348 NA 1.57E-08 mr1170_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
vg1105605348 NA 5.89E-06 mr1184_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
vg1105605348 NA 1.48E-06 mr1488_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
vg1105605348 NA 5.15E-17 mr1557_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
vg1105605348 NA 1.43E-06 mr1779_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