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Detailed information for vg0909301676:

Variant ID: vg0909301676 (JBrowse)Variation Type: INDEL
Chromosome: chr09Position: 9301676
Reference Allele: AAlternative Allele: G,AGTTG
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.71, A: 0.29, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:


TCTATTATCACGAAACTACAGGTCAATGCTAAAACCTGTAGTTTTGTGATAATGAAGACACTAAACTTGTAGTTTTGGGATAAATGAAGATATTAAATCT[A/G,AGTTG]
TAGTTTTGTGAAACAAATTCTTAAATATGTAATTTTGTGAAATATTGTACAAAGTCCATGTAGTTTTGTGATAAACGAAGGCACTGAATCTGTAGTTTTG

Reverse complement sequence

CAAAACTACAGATTCAGTGCCTTCGTTTATCACAAAACTACATGGACTTTGTACAATATTTCACAAAATTACATATTTAAGAATTTGTTTCACAAAACTA[T/C,CAACT]
AGATTTAATATCTTCATTTATCCCAAAACTACAAGTTTAGTGTCTTCATTATCACAAAACTACAGGTTTTAGCATTGACCTGTAGTTTCGTGATAATAGA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 67.70% 29.80% 0.34% 0.00% AGTTG: 2.16%
All Indica  2759 90.90% 8.40% 0.54% 0.00% AGTTG: 0.07%
All Japonica  1512 25.90% 74.00% 0.00% 0.00% AGTTG: 0.13%
Aus  269 85.90% 2.20% 0.00% 0.00% AGTTG: 11.90%
Indica I  595 92.60% 6.40% 1.01% 0.00% NA
Indica II  465 98.30% 1.50% 0.22% 0.00% NA
Indica III  913 83.60% 16.00% 0.44% 0.00% NA
Indica Intermediate  786 93.90% 5.30% 0.51% 0.00% AGTTG: 0.25%
Temperate Japonica  767 12.90% 87.10% 0.00% 0.00% NA
Tropical Japonica  504 37.70% 62.30% 0.00% 0.00% NA
Japonica Intermediate  241 42.30% 56.80% 0.00% 0.00% AGTTG: 0.83%
VI/Aromatic  96 24.00% 16.70% 0.00% 0.00% AGTTG: 59.38%
Intermediate  90 48.90% 40.00% 1.11% 0.00% AGTTG: 10.00%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0909301676 A -> G LOC_Os09g15260-LOC_Os09g15270 intergenic_region ; MODIFIER silent_mutation Average:23.144; most accessible tissue: Callus, score: 46.034 N N N N
vg0909301676 A -> AGTTG LOC_Os09g15260-LOC_Os09g15270 intergenic_region ; MODIFIER silent_mutation Average:23.144; most accessible tissue: Callus, score: 46.034 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0909301676 3.13E-06 NA mr1133_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
vg0909301676 1.06E-06 NA mr1133_2 Jap_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
vg0909301676 NA 9.10E-07 mr1263_2 Jap_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
vg0909301676 NA 1.63E-07 mr1727_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