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Detailed information for vg1221621923:

Variant ID: vg1221621923 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 21621923
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGTCAGAGCATGCTGCTGCGTGCTATGCTGATCGTTATCTCTTGATATTTGGCGGGGGTTCTCATTCTACATGTTTCAGTGATCTACATCTCCTTGACAT[G/T]
CAGACGGTGAGAATTGAATCTTTTCTTTAGAGCTGGTATTCACTACTTTAGGAAGTCCAAATAAATGGTTATCTGCTAATTGCAGATGGAATGGTCAAGA

Reverse complement sequence

TCTTGACCATTCCATCTGCAATTAGCAGATAACCATTTATTTGGACTTCCTAAAGTAGTGAATACCAGCTCTAAAGAAAAGATTCAATTCTCACCGTCTG[C/A]
ATGTCAAGGAGATGTAGATCACTGAAACATGTAGAATGAGAACCCCCGCCAAATATCAAGAGATAACGATCAGCATAGCACGCAGCAGCATGCTCTGACC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.10% 1.80% 0.11% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 94.00% 5.70% 0.33% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 91.50% 8.00% 0.52% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 90.00% 9.50% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg1221621923 G -> T LOC_Os12g35560.1 missense_variant ; p.Met258Ile; MODERATE nonsynonymous_codon ; M258I Average:63.015; most accessible tissue: Minghui63 flag leaf, score: 75.341 unknown unknown DELETERIOUS 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1221621923 6.17E-06 6.17E-06 mr1198 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
vg1221621923 NA 1.68E-06 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
vg1221621923 7.80E-06 5.23E-06 mr1222 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
vg1221621923 3.45E-06 3.45E-06 mr1275 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
vg1221621923 2.61E-06 2.61E-06 mr1284 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
vg1221621923 NA 1.22E-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
vg1221621923 NA 3.10E-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
vg1221621923 NA 6.30E-06 mr1359 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
vg1221621923 3.19E-07 3.19E-07 mr1370 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