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Detailed information for vg1005927955:

Variant ID: vg1005927955 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 5927955
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GAAAGTGTTAGCTAAGACCCGGCTCTTTGTGGGCTCCTCAATAGAGAGTAGAATCCACTCAAGGATTCGAACTTCGGGGAACAACTCATCTTGCAAAAAC[T/A]
TCGGTGATATCACTTTTCCTCTCCTCACTTCTAGTCTTGCTTACTTGTGCCGCTATAGATATAGTTGATGGTTGAGCTTGTTATTCTTATTTGTGGGAAG

Reverse complement sequence

CTTCCCACAAATAAGAATAACAAGCTCAACCATCAACTATATCTATAGCGGCACAAGTAAGCAAGACTAGAAGTGAGGAGAGGAAAAGTGATATCACCGA[A/T]
GTTTTTGCAAGATGAGTTGTTCCCCGAAGTTCGAATCCTTGAGTGGATTCTACTCTCTATTGAGGAGCCCACAAAGAGCCGGGTCTTAGCTAACACTTTC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 59.60% 3.40% 27.72% 9.25% NA
All Indica  2759 49.00% 3.80% 35.99% 11.20% NA
All Japonica  1512 77.20% 2.80% 14.48% 5.49% NA
Aus  269 70.60% 5.20% 24.16% 0.00% NA
Indica I  595 33.60% 2.20% 54.96% 9.24% NA
Indica II  465 47.30% 5.20% 35.48% 12.04% NA
Indica III  913 63.00% 4.20% 20.48% 12.38% NA
Indica Intermediate  786 45.50% 3.70% 39.95% 10.81% NA
Temperate Japonica  767 94.00% 0.50% 3.52% 1.96% NA
Tropical Japonica  504 55.60% 6.20% 28.17% 10.12% NA
Japonica Intermediate  241 68.90% 3.30% 20.75% 7.05% NA
VI/Aromatic  96 51.00% 1.00% 11.46% 36.46% NA
Intermediate  90 63.30% 1.10% 24.44% 11.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1005927955 T -> A LOC_Os10g10720-LOC_Os10g10724 intergenic_region ; MODIFIER silent_mutation Average:42.995; most accessible tissue: Minghui63 panicle, score: 66.554 N N N N
vg1005927955 T -> DEL N N silent_mutation Average:42.995; most accessible tissue: Minghui63 panicle, score: 66.554 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1005927955 NA 8.52E-06 mr1127 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
vg1005927955 NA 7.21E-06 mr1127 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
vg1005927955 NA 8.61E-06 mr1412 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
vg1005927955 2.36E-08 2.36E-08 mr1412 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
vg1005927955 NA 1.85E-07 mr1723_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