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Detailed information for vg0304878960:

Variant ID: vg0304878960 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 4878960
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AACCCTCTATTAATGGAATTTGGTTTATTTTTTGTTCCACCAAAAATGTTTCACCTAGTGTACTCACAATGTTTCACTATGTATAGATCTAATGTTGCTG[C/T]
AGTGAACTAAAATATTCCATTGCAAAAAAAACCCACATATTTTGGAAACTCCCTATTAAGGGAATTCGTTTTATTTTTTGTTCTACCAAAAAAATGTTTC

Reverse complement sequence

GAAACATTTTTTTGGTAGAACAAAAAATAAAACGAATTCCCTTAATAGGGAGTTTCCAAAATATGTGGGTTTTTTTTGCAATGGAATATTTTAGTTCACT[G/A]
CAGCAACATTAGATCTATACATAGTGAAACATTGTGAGTACACTAGGTGAAACATTTTTGGTGGAACAAAAAATAAACCAAATTCCATTAATAGAGGGTT

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 97.80% 0.50% 0.95% 0.78% NA
All Indica  2759 99.10% 0.00% 0.07% 0.80% NA
All Japonica  1512 95.90% 1.50% 2.58% 0.07% NA
Aus  269 99.30% 0.00% 0.74% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.00% 0.00% 0.22% NA
Indica III  913 97.50% 0.00% 0.22% 2.30% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 92.30% 2.90% 4.69% 0.13% NA
Tropical Japonica  504 99.80% 0.00% 0.20% 0.00% NA
Japonica Intermediate  241 99.20% 0.00% 0.83% 0.00% NA
VI/Aromatic  96 85.40% 0.00% 1.04% 13.54% NA
Intermediate  90 97.80% 0.00% 1.11% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0304878960 C -> T LOC_Os03g09810.1 intron_variant ; MODIFIER silent_mutation Average:47.523; most accessible tissue: Minghui63 panicle, score: 73.225 N N N N
vg0304878960 C -> DEL N N silent_mutation Average:47.523; most accessible tissue: Minghui63 panicle, score: 73.225 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0304878960 NA 2.09E-06 mr1062 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
vg0304878960 3.80E-06 6.46E-09 mr1210 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
vg0304878960 NA 2.11E-06 mr1305 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
vg0304878960 NA 6.75E-06 mr1358 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
vg0304878960 NA 6.07E-10 mr1585 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
vg0304878960 NA 1.45E-08 mr1586 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
vg0304878960 NA 2.59E-06 mr1765 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
vg0304878960 NA 3.01E-06 mr1305_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
vg0304878960 NA 1.64E-07 mr1585_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
vg0304878960 NA 6.87E-08 mr1693_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