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Detailed information for vg1021514492:

Variant ID: vg1021514492 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 21514492
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AATGTGATGACCACTAAGACAAGTTGGATACCTCCTTTACAACATAAATAACCTAATCAAGAGGTCACTAAGAGGTGAAAAGGCTACTCACTTGAGGTGG[C/T]
CGTTGCCATCCCGGCCTTCGCATCAAGAGTTTGATCCACATTGTCAGACGAAACATGTGGTTCAAAATCGAGTACCGGAATCATCGCCAGTGACTCAGGC

Reverse complement sequence

GCCTGAGTCACTGGCGATGATTCCGGTACTCGATTTTGAACCACATGTTTCGTCTGACAATGTGGATCAAACTCTTGATGCGAAGGCCGGGATGGCAACG[G/A]
CCACCTCAAGTGAGTAGCCTTTTCACCTCTTAGTGACCTCTTGATTAGGTTATTTATGTTGTAAAGGAGGTATCCAACTTGTCTTAGTGGTCATCACATT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 62.20% 37.40% 0.44% 0.00% NA
All Indica  2759 96.00% 3.40% 0.62% 0.00% NA
All Japonica  1512 1.30% 98.70% 0.00% 0.00% NA
Aus  269 79.90% 18.60% 1.49% 0.00% NA
Indica I  595 94.80% 4.70% 0.50% 0.00% NA
Indica II  465 94.80% 4.70% 0.43% 0.00% NA
Indica III  913 98.50% 1.00% 0.55% 0.00% NA
Indica Intermediate  786 94.80% 4.30% 0.89% 0.00% NA
Temperate Japonica  767 1.20% 98.80% 0.00% 0.00% NA
Tropical Japonica  504 1.20% 98.80% 0.00% 0.00% NA
Japonica Intermediate  241 1.70% 98.30% 0.00% 0.00% NA
VI/Aromatic  96 14.60% 85.40% 0.00% 0.00% NA
Intermediate  90 46.70% 53.30% 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
vg1021514492 C -> T LOC_Os10g40190.1 missense_variant ; p.Ala574Thr; MODERATE nonsynonymous_codon ; A574T Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 unknown unknown TOLERATED 1.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1021514492 NA 9.09E-11 mr1325 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
vg1021514492 NA 7.20E-13 mr1326 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
vg1021514492 1.07E-06 NA mr1682 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
vg1021514492 NA 5.45E-22 mr1698 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
vg1021514492 NA 1.54E-08 mr1322_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
vg1021514492 NA 1.62E-07 mr1623_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