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Detailed information for vg0224605253:

Variant ID: vg0224605253 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 24605253
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTTGTGCTGGAATGAGGTGGGCGAAGCACTGGTATTCGGTCCTGACGTACTCAAGGCAGCAGAAGAACAAGTTAAACTGATCCGAGAACGTTTAAAGACA[G/A]
CGCAGAACCGTCAGAAGAATTACGCGGACAATCGAAGGCGTGACCTTGAGTTCGAAAAAGGAGATCATGTGTACCTGCGGGTATCGCCTCTCCGTGGTAT

Reverse complement sequence

ATACCACGGAGAGGCGATACCCGCAGGTACACATGATCTCCTTTTTCGAACTCAAGGTCACGCCTTCGATTGTCCGCGTAATTCTTCTGACGGTTCTGCG[C/T]
TGTCTTTAAACGTTCTCGGATCAGTTTAACTTGTTCTTCTGCTGCCTTGAGTACGTCAGGACCGAATACCAGTGCTTCGCCCACCTCATTCCAGCACAAG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 82.10% 3.30% 1.18% 13.42% NA
All Indica  2759 81.00% 5.40% 1.27% 12.32% NA
All Japonica  1512 79.50% 0.20% 1.39% 18.92% NA
Aus  269 99.30% 0.00% 0.00% 0.74% NA
Indica I  595 45.20% 18.00% 2.02% 34.79% NA
Indica II  465 84.30% 6.00% 2.80% 6.88% NA
Indica III  913 98.10% 0.00% 0.00% 1.86% NA
Indica Intermediate  786 86.30% 1.80% 1.27% 10.69% NA
Temperate Japonica  767 70.40% 0.40% 1.43% 27.77% NA
Tropical Japonica  504 94.00% 0.00% 1.19% 4.76% NA
Japonica Intermediate  241 78.00% 0.00% 1.66% 20.33% NA
VI/Aromatic  96 97.90% 0.00% 0.00% 2.08% NA
Intermediate  90 93.30% 2.20% 0.00% 4.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0224605253 G -> A LOC_Os02g40570.1 missense_variant ; p.Ala1660Thr; MODERATE nonsynonymous_codon ; A1660T Average:17.291; most accessible tissue: Minghui63 panicle, score: 38.588 benign 0.573 DELETERIOUS 0.02
vg0224605253 G -> DEL LOC_Os02g40570.1 N frameshift_variant Average:17.291; most accessible tissue: Minghui63 panicle, score: 38.588 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0224605253 5.85E-13 4.20E-16 mr1191 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
vg0224605253 2.17E-12 1.32E-12 mr1191 Ind_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
vg0224605253 1.10E-12 1.26E-15 mr1644 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
vg0224605253 1.67E-11 2.61E-12 mr1644 Ind_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
vg0224605253 NA 9.45E-08 mr1662 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
vg0224605253 NA 6.84E-08 mr1662 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
vg0224605253 6.94E-14 1.13E-22 mr1191_2 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
vg0224605253 2.00E-12 2.81E-17 mr1191_2 Ind_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
vg0224605253 NA 9.96E-06 mr1566_2 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
vg0224605253 NA 1.38E-06 mr1662_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
vg0224605253 NA 5.12E-06 mr1662_2 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
vg0224605253 4.41E-06 NA mr1897_2 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