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Detailed information for vg0606407151:

Variant ID: vg0606407151 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 6407151
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 309. )

Flanking Sequence (100 bp) in Reference Genome:


ACTTACTGTGTACATGCACAGGTGATGTTGTGCACAAGAACTATACTAATCCTTGAGACTTCAATCAATTCACATCAACCCCAAGAATTCAACAATATGC[A/C]
TTAACAAAAGACTATTCAATGGAAAAGTATAAAATTTGTTATAGGGCTCTGATGGTGGCAAAGGGATGGAATCCTTTGAGGAGTTCAACTATTCACTCTA

Reverse complement sequence

TAGAGTGAATAGTTGAACTCCTCAAAGGATTCCATCCCTTTGCCACCATCAGAGCCCTATAACAAATTTTATACTTTTCCATTGAATAGTCTTTTGTTAA[T/G]
GCATATTGTTGAATTCTTGGGGTTGATGTGAATTGATTGAAGTCTCAAGGATTAGTATAGTTCTTGTGCACAACATCACCTGTGCATGTACACAGTAAGT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 92.10% 5.50% 2.41% 0.00% NA
All Indica  2759 98.90% 0.00% 1.01% 0.00% NA
All Japonica  1512 77.40% 17.10% 5.56% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 97.30% 0.00% 2.69% 0.00% NA
Indica II  465 99.80% 0.00% 0.22% 0.00% NA
Indica III  913 99.90% 0.00% 0.11% 0.00% NA
Indica Intermediate  786 98.60% 0.10% 1.27% 0.00% NA
Temperate Japonica  767 61.00% 28.90% 10.04% 0.00% NA
Tropical Japonica  504 98.40% 1.40% 0.20% 0.00% NA
Japonica Intermediate  241 85.50% 12.00% 2.49% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 95.60% 2.20% 2.22% 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
vg0606407151 A -> C LOC_Os06g11990.1 intron_variant ; MODIFIER silent_mutation Average:61.904; most accessible tissue: Minghui63 root, score: 72.958 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0606407151 1.41E-06 NA mr1310_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
vg0606407151 NA 5.39E-08 mr1681_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
vg0606407151 8.79E-07 1.97E-13 mr1959_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
vg0606407151 NA 2.50E-06 mr1959_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