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Detailed information for vg1105865316:

Variant ID: vg1105865316 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 5865316
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.94, T: 0.05, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:


ATAATGCCACATCGGCATAAGCAAAATGATTCCTCTGCATTATATTCCTCCAGGAAGAACATTGCGCTGTAGCCTTTTATAAACAAAACACACGATAGTA[A/T]
TAATTAATTACCTCACCAATGATAGCTTCTTTCTCGTTAATTTGATTGATGATTTCCACTATATTAGGCCTATTTTCCCTATCAGTCTCCATGCATTTCA

Reverse complement sequence

TGAAATGCATGGAGACTGATAGGGAAAATAGGCCTAATATAGTGGAAATCATCAATCAAATTAACGAGAAAGAAGCTATCATTGGTGAGGTAATTAATTA[T/A]
TACTATCGTGTGTTTTGTTTATAAAAGGCTACAGCGCAATGTTCTTCCTGGAGGAATATAATGCAGAGGAATCATTTTGCTTATGCCGATGTGGCATTAT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 88.50% 11.40% 0.08% 0.00% NA
All Indica  2759 92.60% 7.20% 0.14% 0.00% NA
All Japonica  1512 93.50% 6.50% 0.00% 0.00% NA
Aus  269 16.70% 83.30% 0.00% 0.00% NA
Indica I  595 97.50% 2.40% 0.17% 0.00% NA
Indica II  465 98.70% 1.30% 0.00% 0.00% NA
Indica III  913 86.50% 13.40% 0.11% 0.00% NA
Indica Intermediate  786 92.40% 7.40% 0.25% 0.00% NA
Temperate Japonica  767 93.70% 6.30% 0.00% 0.00% NA
Tropical Japonica  504 95.60% 4.40% 0.00% 0.00% NA
Japonica Intermediate  241 88.40% 11.60% 0.00% 0.00% NA
VI/Aromatic  96 87.50% 12.50% 0.00% 0.00% NA
Intermediate  90 92.20% 7.80% 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
vg1105865316 A -> T LOC_Os11g10670-LOC_Os11g10710 intergenic_region ; MODIFIER silent_mutation Average:37.452; most accessible tissue: Callus, score: 80.287 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1105865316 NA 2.98E-08 mr1465 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
vg1105865316 4.59E-06 NA mr1203_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
vg1105865316 1.16E-07 NA mr1613_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
vg1105865316 1.41E-06 NA mr1613_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