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Detailed information for vg0800427985:

Variant ID: vg0800427985 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 427985
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTCCACCATGCGTATATATGTGCATGCATCGCCGGCCGGACTGACTGACAGTAGTAGCAGCTACTACTCCCTCCGTCCCAAAAAAACAAACCCTGGTTTC[T/C]
GTGTCCAACGTACGTCTGTCTTATTTGAAAAAATTATGAAAAAAATTAAAAAGATAAGTCACGCATAAAGTATTAATCATATTTTATCATCTAACAACAA

Reverse complement sequence

TTGTTGTTAGATGATAAAATATGATTAATACTTTATGCGTGACTTATCTTTTTAATTTTTTTCATAATTTTTTCAAATAAGACAGACGTACGTTGGACAC[A/G]
GAAACCAGGGTTTGTTTTTTTGGGACGGAGGGAGTAGTAGCTGCTACTACTGTCAGTCAGTCCGGCCGGCGATGCATGCACATATATACGCATGGTGGAG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 51.80% 38.40% 0.89% 8.84% NA
All Indica  2759 75.10% 8.80% 1.09% 14.93% NA
All Japonica  1512 1.50% 98.20% 0.13% 0.20% NA
Aus  269 94.10% 5.20% 0.37% 0.37% NA
Indica I  595 63.70% 9.20% 2.18% 24.87% NA
Indica II  465 85.60% 5.40% 1.08% 7.96% NA
Indica III  913 78.00% 8.30% 0.77% 12.92% NA
Indica Intermediate  786 74.30% 11.20% 0.64% 13.87% NA
Temperate Japonica  767 1.40% 98.60% 0.00% 0.00% NA
Tropical Japonica  504 1.00% 98.00% 0.40% 0.60% NA
Japonica Intermediate  241 2.50% 97.50% 0.00% 0.00% NA
VI/Aromatic  96 61.50% 31.20% 7.29% 0.00% NA
Intermediate  90 46.70% 48.90% 2.22% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0800427985 T -> C LOC_Os08g01700-LOC_Os08g01710 intergenic_region ; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0800427985 T -> DEL N N silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0800427985 NA 7.23E-24 mr1102 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
vg0800427985 NA 4.72E-12 mr1170 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
vg0800427985 NA 4.06E-26 mr1223 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
vg0800427985 NA 2.05E-40 mr1480 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
vg0800427985 NA 7.72E-12 mr1636 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
vg0800427985 NA 7.38E-15 mr1653 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
vg0800427985 NA 3.48E-28 mr1723 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
vg0800427985 NA 1.35E-13 mr1909 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
vg0800427985 NA 9.37E-25 mr1653_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