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Detailed information for vg0506207863:

Variant ID: vg0506207863 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 6207863
Reference Allele: CAlternative Allele: A,T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGAGCGCAAGCGCCGGGAGAAGCTCAACGATAGCTTCAAGGCTCTCAGGGACGTGCTCCCACCCGCCACCAAGGTCCGTCTACTTACCGACCAATTTAAT[C/A,T]
TAAAAGCTTACGTAAATATAGAATCTCGAGCAAAATCTGTTGTCTTGCTTGACGAAAGATTCTCACATAATCCCAAACTCTCTCAAATCTAGATTGTTAC

Reverse complement sequence

GTAACAATCTAGATTTGAGAGAGTTTGGGATTATGTGAGAATCTTTCGTCAAGCAAGACAACAGATTTTGCTCGAGATTCTATATTTACGTAAGCTTTTA[G/T,A]
ATTAAATTGGTCGGTAAGTAGACGGACCTTGGTGGCGGGTGGGAGCACGTCCCTGAGAGCCTTGAAGCTATCGTTGAGCTTCTCCCGGCGCTTGCGCTCC

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 97.20% 1.90% 0.53% 0.00% A: 0.36%
All Indica  2759 99.20% 0.10% 0.14% 0.00% A: 0.62%
All Japonica  1512 92.80% 5.80% 1.39% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 97.80% 0.00% 0.33% 0.00% A: 1.86%
Indica Intermediate  786 99.60% 0.30% 0.13% 0.00% NA
Temperate Japonica  767 99.00% 0.90% 0.13% 0.00% NA
Tropical Japonica  504 81.90% 14.30% 3.77% 0.00% NA
Japonica Intermediate  241 95.90% 3.70% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 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
vg0506207863 C -> T LOC_Os05g11070.1 intron_variant ; MODIFIER silent_mutation Average:60.697; most accessible tissue: Minghui63 panicle, score: 77.956 N N N N
vg0506207863 C -> A LOC_Os05g11070.1 intron_variant ; MODIFIER silent_mutation Average:60.697; most accessible tissue: Minghui63 panicle, score: 77.956 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0506207863 7.25E-06 1.68E-07 mr1218 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
vg0506207863 NA 5.80E-06 mr1350 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
vg0506207863 8.95E-10 6.72E-13 mr1422 Jap_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
vg0506207863 1.78E-07 1.56E-12 mr1583 Jap_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
vg0506207863 2.67E-07 5.51E-10 mr1218_2 Jap_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
vg0506207863 1.21E-09 6.18E-12 mr1422_2 Jap_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
vg0506207863 4.89E-07 2.79E-09 mr1583_2 Jap_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
vg0506207863 2.82E-15 4.88E-22 mr1850_2 Jap_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