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Detailed information for vg0208100222:

Variant ID: vg0208100222 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 8100222
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCCTAGCCCCATCAGGGAAATTGCCACTCCTAGGCCTTATTTAGTTCTCAATTTTTTTTCCTAAAAACGTCATATTGAATCTTTAGTCATATGCATAGAG[C/T]
ATTAAATATAGATAAAATGATAAACTAATTGTACAGTTTACATGGAAATCAAGAGACGAATCTTTTGAGCCTAATTCGTCCATGATTAGCAATAAGTGCT

Reverse complement sequence

AGCACTTATTGCTAATCATGGACGAATTAGGCTCAAAAGATTCGTCTCTTGATTTCCATGTAAACTGTACAATTAGTTTATCATTTTATCTATATTTAAT[G/A]
CTCTATGCATATGACTAAAGATTCAATATGACGTTTTTAGGAAAAAAAATTGAGAACTAAATAAGGCCTAGGAGTGGCAATTTCCCTGATGGGGCTAGGG

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 95.90% 4.10% 0.08% 0.00% NA
All Indica  2759 93.30% 6.50% 0.14% 0.00% NA
All Japonica  1512 99.50% 0.50% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 95.00% 5.00% 0.00% 0.00% NA
Indica II  465 77.80% 21.70% 0.43% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 93.50% 6.20% 0.25% 0.00% NA
Temperate Japonica  767 99.50% 0.50% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 1.20% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 95.60% 4.40% 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
vg0208100222 C -> T LOC_Os02g14680-LOC_Os02g14700 intergenic_region ; MODIFIER silent_mutation Average:41.768; most accessible tissue: Minghui63 root, score: 60.831 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0208100222 NA 4.02E-06 mr1305 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
vg0208100222 2.25E-07 NA mr1401 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
vg0208100222 5.09E-07 1.46E-06 mr1401 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
vg0208100222 NA 1.97E-06 mr1586 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