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Detailed information for vg0223219897:

Variant ID: vg0223219897 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 23219897
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATTTGTCTTGTGAGGGTTTATATTACCGGTTGACCACTAAATTTCGAGCCTCATCGGTATCATGTTTTTTGATAAATTTTGATCGGTTTCGGATAAATTT[C/T]
GACTGAATTTCGACCAAATCTACTGTTTAACCTTCGAAATTCCAATCGAAACTTAATTTTGAGCCGCGTCGAAACGTCGAAATTTCGCGGAACTCGACCG

Reverse complement sequence

CGGTCGAGTTCCGCGAAATTTCGACGTTTCGACGCGGCTCAAAATTAAGTTTCGATTGGAATTTCGAAGGTTAAACAGTAGATTTGGTCGAAATTCAGTC[G/A]
AAATTTATCCGAAACCGATCAAAATTTATCAAAAAACATGATACCGATGAGGCTCGAAATTTAGTGGTCAACCGGTAATATAAACCCTCACAAGACAAAT

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 95.70% 4.20% 0.08% 0.00% NA
All Indica  2759 97.60% 2.40% 0.00% 0.00% NA
All Japonica  1512 91.30% 8.50% 0.20% 0.00% NA
Aus  269 99.60% 0.00% 0.37% 0.00% NA
Indica I  595 99.70% 0.30% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.20% 0.80% 0.00% 0.00% NA
Indica Intermediate  786 92.90% 7.10% 0.00% 0.00% NA
Temperate Japonica  767 96.90% 2.90% 0.26% 0.00% NA
Tropical Japonica  504 94.80% 5.00% 0.20% 0.00% NA
Japonica Intermediate  241 66.40% 33.60% 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
vg0223219897 C -> T LOC_Os02g38392.1 3_prime_UTR_variant ; 146.0bp to feature; MODIFIER silent_mutation Average:53.491; most accessible tissue: Minghui63 panicle, score: 64.459 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0223219897 NA 2.51E-07 mr1117 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
vg0223219897 NA 5.50E-06 mr1240 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
vg0223219897 NA 5.46E-08 mr1693 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
vg0223219897 NA 2.41E-07 mr1117_2 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
vg0223219897 NA 1.76E-07 mr1496_2 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
vg0223219897 NA 4.58E-07 mr1519_2 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
vg0223219897 2.52E-07 7.98E-07 mr1750_2 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