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Detailed information for vg0616953325:

Variant ID: vg0616953325 (JBrowse)Variation Type: INDEL
Chromosome: chr06Position: 16953325
Reference Allele: GAlternative Allele: GTCA,A
Primary Allele: GTCASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 204. )

Flanking Sequence (100 bp) in Reference Genome:


AATTTGGATTGACCACATGTTTTTTTGATTGGCTGCAATTAATAAGCATGAAATAGGGACTGCATATGAATTTTGAACTGACTACAATAAAGCTATCTTC[G/GTCA,A]
TCATCAAGGGGAATGGCATCATTGTAATCTACCTTCCTTTTGTTTGACTTGTCAAGCTGCTCCAAATATGCATGCCACTTTGGTTGGTTTTTAAGTTCAT

Reverse complement sequence

ATGAACTTAAAAACCAACCAAAGTGGCATGCATATTTGGAGCAGCTTGACAAGTCAAACAAAAGGAAGGTAGATTACAATGATGCCATTCCCCTTGATGA[C/TGAC,T]
GAAGATAGCTTTATTGTAGTCAGTTCAAAATTCATATGCAGTCCCTATTTCATGCTTATTAATTGCAGCCAATCAAAAAAACATGTGGTCAATCCAAATT

Allele Frequencies:

Populations Population SizeFrequency of GTCA(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 64.50% 29.40% 0.08% 0.00% A: 5.99%
All Indica  2759 97.60% 1.70% 0.04% 0.00% A: 0.58%
All Japonica  1512 2.80% 86.60% 0.00% 0.00% A: 10.65%
Aus  269 91.40% 1.90% 0.00% 0.00% A: 6.69%
Indica I  595 97.50% 2.50% 0.00% 0.00% NA
Indica II  465 97.40% 1.10% 0.00% 0.00% A: 1.51%
Indica III  913 99.20% 0.20% 0.11% 0.00% A: 0.44%
Indica Intermediate  786 96.10% 3.30% 0.00% 0.00% A: 0.64%
Temperate Japonica  767 3.50% 96.20% 0.00% 0.00% A: 0.26%
Tropical Japonica  504 2.00% 70.00% 0.00% 0.00% A: 27.98%
Japonica Intermediate  241 2.10% 90.50% 0.00% 0.00% A: 7.47%
VI/Aromatic  96 17.70% 1.00% 0.00% 0.00% A: 81.25%
Intermediate  90 55.60% 30.00% 3.33% 0.00% A: 11.11%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0616953325 G -> A LOC_Os06g29580.1 intron_variant ; MODIFIER silent_mutation Average:43.505; most accessible tissue: Callus, score: 61.918 N N N N
vg0616953325 G -> GTCA LOC_Os06g29580.1 intron_variant ; MODIFIER silent_mutation Average:43.505; most accessible tissue: Callus, score: 61.918 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0616953325 NA 7.12E-08 mr1930 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
vg0616953325 8.58E-07 NA mr1070_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
vg0616953325 1.93E-09 NA mr1082_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
vg0616953325 2.25E-10 NA mr1083_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
vg0616953325 4.50E-07 NA mr1085_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
vg0616953325 1.59E-06 NA mr1103_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
vg0616953325 7.62E-07 NA mr1104_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
vg0616953325 1.89E-06 NA mr1107_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
vg0616953325 2.48E-07 NA mr1145_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
vg0616953325 1.29E-06 NA mr1226_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
vg0616953325 3.52E-08 3.24E-09 mr1408_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