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Search for Variation information by Variation ID:

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

Detailed information for vg0715983729:

Variant ID: vg0715983729 (JBrowse)Variation Type: INDEL
Chromosome: chr07Position: 15983729
Reference Allele: TAlternative Allele: TAATCTTTTTATTGAAGGGAAACCTTGTCATG,G
Primary Allele: TSecondary Allele: TAATCTTTTTATTGAAGGGA AACCTTGTCATG

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:


TACTTACTATAACATTACCTTTTCTAAGTTAGAATCATGCATTCGCACGTTGATTGATTTGTCTTTTTTTAACGATCTGTTTTGAATCTTACCTTGTCAT[T/TAATCTTTTTATTGAAGGGAAACCTTGTCATG,G]
AATCTTGACTTTAATCGTTTCAGTCTGCAGTACTCGGTGAGTTTTTGGTCTCAGGGCGAGCAACACATAAGCTGCTTCAGATGTATGTCCCTTTTGCTGT

Reverse complement sequence

ACAGCAAAAGGGACATACATCTGAAGCAGCTTATGTGTTGCTCGCCCTGAGACCAAAAACTCACCGAGTACTGCAGACTGAAACGATTAAAGTCAAGATT[A/CATGACAAGGTTTCCCTTCAATAAAAAGATTA,C]
ATGACAAGGTAAGATTCAAAACAGATCGTTAAAAAAAGACAAATCAATCAACGTGCGAATGCATGATTCTAACTTAGAAAAGGTAATGTTATAGTAAGTA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of TAATCTTTTTATTGAAGGGA AACCTTGTCATG(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 69.90% 29.50% 0.15% 0.00% G: 0.51%
All Indica  2759 49.70% 49.30% 0.18% 0.00% G: 0.83%
All Japonica  1512 99.30% 0.70% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 49.90% 47.70% 0.50% 0.00% G: 1.85%
Indica II  465 21.30% 76.80% 0.43% 0.00% G: 1.51%
Indica III  913 56.70% 43.30% 0.00% 0.00% NA
Indica Intermediate  786 58.30% 41.10% 0.00% 0.00% G: 0.64%
Temperate Japonica  767 99.10% 0.80% 0.13% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 72.20% 25.60% 1.11% 0.00% G: 1.11%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0715983729 T -> G LOC_Os07g27420.1 downstream_gene_variant ; 2686.0bp to feature; MODIFIER silent_mutation Average:62.836; most accessible tissue: Callus, score: 83.746 N N N N
vg0715983729 T -> G LOC_Os07g27430.1 intron_variant ; MODIFIER silent_mutation Average:62.836; most accessible tissue: Callus, score: 83.746 N N N N
vg0715983729 T -> TAATCTTTTTATTGAAGGGAAACCTTGTCA TG LOC_Os07g27420.1 downstream_gene_variant ; 2687.0bp to feature; MODIFIER silent_mutation Average:62.836; most accessible tissue: Callus, score: 83.746 N N N N
vg0715983729 T -> TAATCTTTTTATTGAAGGGAAACCTTGTCA TG LOC_Os07g27430.1 intron_variant ; MODIFIER silent_mutation Average:62.836; most accessible tissue: Callus, score: 83.746 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0715983729 6.96E-06 6.96E-06 mr1853 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
vg0715983729 NA 3.55E-06 mr1942 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
vg0715983729 NA 5.87E-07 mr1212_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