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Detailed information for vg0419558541:

Variant ID: vg0419558541 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 19558541
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTACACCCTATCGCTATCGGCTGGTATCGGCATCGGCTATTATCGGCTATCGGTTGGAACTACTCCATCGGCTTGTTAGCCGATCGGCTATTTTGATCTA[C/A]
TATTTGCATATCTTGTCAGTTGCAGGATCAAACTGACTGGCACGTCCGCATCTCATCAAGATTTAGACCTGCACAGCAGCTAAGCAGATCTCCCAGGCCA

Reverse complement sequence

TGGCCTGGGAGATCTGCTTAGCTGCTGTGCAGGTCTAAATCTTGATGAGATGCGGACGTGCCAGTCAGTTTGATCCTGCAACTGACAAGATATGCAAATA[G/T]
TAGATCAAAATAGCCGATCGGCTAACAAGCCGATGGAGTAGTTCCAACCGATAGCCGATAATAGCCGATGCCGATACCAGCCGATAGCGATAGGGTGTAA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 96.40% 3.10% 0.51% 0.00% NA
All Indica  2759 99.30% 0.70% 0.04% 0.00% NA
All Japonica  1512 90.70% 8.00% 1.32% 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 98.30% 1.70% 0.00% 0.00% NA
Indica III  913 99.30% 0.50% 0.11% 0.00% NA
Indica Intermediate  786 99.40% 0.60% 0.00% 0.00% NA
Temperate Japonica  767 99.20% 0.00% 0.78% 0.00% NA
Tropical Japonica  504 75.60% 21.80% 2.58% 0.00% NA
Japonica Intermediate  241 95.00% 4.60% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 87.80% 8.90% 3.33% 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
vg0419558541 C -> A LOC_Os04g32500-LOC_Os04g32510 intergenic_region ; MODIFIER silent_mutation Average:27.007; 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
vg0419558541 NA 1.84E-06 mr1422 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
vg0419558541 NA 1.07E-09 mr1583 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
vg0419558541 6.15E-07 6.15E-07 mr1050_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
vg0419558541 2.53E-06 1.08E-07 mr1498_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
vg0419558541 NA 8.60E-07 mr1629_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
vg0419558541 NA 1.18E-07 mr1850_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