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Detailed information for vg0818608910:

Variant ID: vg0818608910 (JBrowse)Variation Type: INDEL
Chromosome: chr08Position: 18608910
Reference Allele: GAlternative Allele: GAATGATGAGAACAAGCGAAGTGGAAAAACGA,A
Primary Allele: GSecondary Allele: GAATGATGAGAACAAGCGAA GTGGAAAAACGA

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:


CTCCCCTCCTCCTGTGTTTGCATCTCTCCCCTCTACAACAAATTGCTCTCCCTATATCTCCATCTTCATAGCTTGGATCAACAAGCGAAGTGGAAAAACG[G/GAATGATGAGAACAAGCGAAGTGGAAAAACGA,A]
AATGATGAGGAGGAGAGGAGTAGGAGGGGTTAGATCGGAGTCTCCCCTATTGTCTCCTCACAAGTTCTCTAAAAAAACCCTAGGTGATGAGGACATCCCA

Reverse complement sequence

TGGGATGTCCTCATCACCTAGGGTTTTTTTAGAGAACTTGTGAGGAGACAATAGGGGAGACTCCGATCTAACCCCTCCTACTCCTCTCCTCCTCATCATT[C/TCGTTTTTCCACTTCGCTTGTTCTCATCATTC,T]
CGTTTTTCCACTTCGCTTGTTGATCCAAGCTATGAAGATGGAGATATAGGGAGAGCAATTTGTTGTAGAGGGGAGAGATGCAAACACAGGAGGAGGGGAG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of GAATGATGAGAACAAGCGAA GTGGAAAAACGA(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 86.20% 13.70% 0.04% 0.00% A: 0.11%
All Indica  2759 76.50% 23.20% 0.07% 0.00% A: 0.18%
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 67.70% 31.80% 0.00% 0.00% A: 0.50%
Indica II  465 99.10% 0.90% 0.00% 0.00% NA
Indica III  913 65.00% 34.90% 0.11% 0.00% NA
Indica Intermediate  786 83.30% 16.30% 0.13% 0.00% A: 0.25%
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 93.30% 6.70% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0818608910 G -> A LOC_Os08g30260-LOC_Os08g30270 intergenic_region ; MODIFIER silent_mutation Average:51.951; most accessible tissue: Zhenshan97 young leaf, score: 73.54 N N N N
vg0818608910 G -> GAATGATGAGAACAAGCGAAGTGGAAAAAC GA LOC_Os08g30260-LOC_Os08g30270 intergenic_region ; MODIFIER silent_mutation Average:51.951; most accessible tissue: Zhenshan97 young leaf, score: 73.54 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0818608910 NA 1.15E-06 mr1096 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
vg0818608910 4.84E-07 NA mr1486 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
vg0818608910 6.29E-08 1.74E-06 mr1486 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
vg0818608910 3.25E-07 NA mr1548 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
vg0818608910 2.14E-07 8.16E-07 mr1548 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
vg0818608910 4.63E-06 NA mr1588 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
vg0818608910 4.63E-06 3.32E-06 mr1588 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
vg0818608910 2.95E-06 NA mr1486_2 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
vg0818608910 1.06E-07 NA mr1588_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
vg0818608910 2.42E-08 2.46E-06 mr1588_2 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