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Detailed information for vg1221533276:

Variant ID: vg1221533276 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 21533276
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTTGGTCATTGTTAAGTTGTGAAATCAAAGTTTCTGCGTGCATTGACATCATCAAGGGATGGTGAGAGCTCCTCTTCAATAAGCCTATTACCCATGGGTA[C/T]
TTGTGGAGAGAAGGTTAGATGAGGCAGGTTATAATCTCTTATGTTGCCACCACTCTTTCCAAAGACACTGGTAAGTTCATGTATTAACAAAGTAAGAAGA

Reverse complement sequence

TCTTCTTACTTTGTTAATACATGAACTTACCAGTGTCTTTGGAAAGAGTGGTGGCAACATAAGAGATTATAACCTGCCTCATCTAACCTTCTCTCCACAA[G/A]
TACCCATGGGTAATAGGCTTATTGAAGAGGAGCTCTCACCATCCCTTGATGATGTCAATGCACGCAGAAACTTTGATTTCACAACTTAACAATGACCAAA

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 97.50% 1.30% 1.18% 0.00% NA
All Indica  2759 96.60% 2.10% 1.38% 0.00% NA
All Japonica  1512 99.70% 0.20% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 86.20% 8.20% 5.55% 0.00% NA
Indica II  465 99.60% 0.00% 0.43% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 98.60% 1.00% 0.38% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.40% 0.41% 0.00% NA
VI/Aromatic  96 84.40% 0.00% 15.62% 0.00% NA
Intermediate  90 97.80% 0.00% 2.22% 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
vg1221533276 C -> T LOC_Os12g35410.1 missense_variant ; p.Val997Ile; MODERATE nonsynonymous_codon ; V997I Average:56.741; most accessible tissue: Minghui63 flag leaf, score: 82.053 unknown unknown TOLERATED 0.44

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1221533276 6.54E-07 NA mr1038 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
vg1221533276 4.48E-06 NA mr1038 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
vg1221533276 4.98E-08 NA mr1038_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
vg1221533276 5.49E-07 NA mr1038_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
vg1221533276 1.17E-06 NA mr1141_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
vg1221533276 5.20E-06 NA mr1141_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
vg1221533276 4.17E-07 NA mr1389_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
vg1221533276 2.52E-06 NA mr1389_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