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Detailed information for vg0906975807:

Variant ID: vg0906975807 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 6975807
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:


GGTCGCCGAGGAGGAGGCCTCGCCCTCGATCTTCATGTGGTGGAACGCGAAGGGTGGGGAATTCCCCCCCCCCTCCCCCGCGTCAATTGTGGCCTAGGTG[C/T]
CGATGTCAACCCCAGCAAGGCCAAGGCGCAGGAGGCGGGTGCCTACCCAACCATCGCGTAGGAGGAGGGAGAAAGCTTTGAAACGTGTACGAAAATTGTT

Reverse complement sequence

AACAATTTTCGTACACGTTTCAAAGCTTTCTCCCTCCTCCTACGCGATGGTTGGGTAGGCACCCGCCTCCTGCGCCTTGGCCTTGCTGGGGTTGACATCG[G/A]
CACCTAGGCCACAATTGACGCGGGGGAGGGGGGGGGGAATTCCCCACCCTTCGCGTTCCACCACATGAAGATCGAGGGCGAGGCCTCCTCCTCGGCGACC

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 97.40% 1.70% 0.93% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 92.00% 5.20% 2.84% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 84.90% 9.80% 5.35% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 97.90% 1.20% 0.83% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 0.00% 1.11% 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
vg0906975807 C -> T LOC_Os09g12250.1 intron_variant ; MODIFIER silent_mutation Average:66.088; most accessible tissue: Callus, score: 92.096 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0906975807 9.88E-08 4.90E-09 mr1060_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
vg0906975807 NA 1.80E-06 mr1321_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
vg0906975807 9.79E-06 2.64E-06 mr1332_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
vg0906975807 NA 1.24E-06 mr1354_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
vg0906975807 1.63E-07 1.63E-07 mr1371_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
vg0906975807 1.58E-08 1.58E-08 mr1499_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
vg0906975807 NA 2.54E-06 mr1576_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
vg0906975807 4.64E-06 1.89E-07 mr1621_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
vg0906975807 3.17E-06 3.17E-06 mr1647_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
vg0906975807 NA 2.71E-07 mr1902_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