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Detailed information for vg0404379553:

Variant ID: vg0404379553 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 4379553
Reference Allele: CAlternative Allele: T,A
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 96. )

Flanking Sequence (100 bp) in Reference Genome:


TGGAAACTGCCGGTGCTGGTAATGGAGGGAATAGGCGGCAACTGATTGAAACGGGTGATCGTCGTGGTTGACGATTCCTCCACGCCGGCTCCATCTGCCA[C/T,A]
CGTGGATGCTCTCAGTGTGGTTGGGGATGACAGATCTAGAAGTCACTCATGGCTCCATCCGTTCTAGTGACGCAGCAACCTAGCCGTCACAGGCTAAAAG

Reverse complement sequence

CTTTTAGCCTGTGACGGCTAGGTTGCTGCGTCACTAGAACGGATGGAGCCATGAGTGACTTCTAGATCTGTCATCCCCAACCACACTGAGAGCATCCACG[G/A,T]
TGGCAGATGGAGCCGGCGTGGAGGAATCGTCAACCACGACGATCACCCGTTTCAATCAGTTGCCGCCTATTCCCTCCATTACCAGCACCGGCAGTTTCCA

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 68.60% 19.40% 0.17% 11.83% NA
All Indica  2759 58.90% 32.30% 0.25% 8.52% NA
All Japonica  1512 87.40% 0.50% 0.07% 12.04% NA
Aus  269 50.20% 0.00% 0.00% 49.81% NA
Indica I  595 5.20% 90.60% 0.17% 4.03% NA
Indica II  465 93.10% 6.70% 0.00% 0.22% NA
Indica III  913 72.50% 14.50% 0.33% 12.71% NA
Indica Intermediate  786 63.50% 24.20% 0.38% 11.96% NA
Temperate Japonica  767 95.70% 0.10% 0.00% 4.17% NA
Tropical Japonica  504 81.20% 0.40% 0.20% 18.25% NA
Japonica Intermediate  241 74.30% 1.70% 0.00% 24.07% NA
VI/Aromatic  96 94.80% 2.10% 0.00% 3.12% NA
Intermediate  90 78.90% 15.60% 0.00% 5.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0404379553 C -> DEL N N silent_mutation Average:41.636; most accessible tissue: Zhenshan97 flag leaf, score: 71.238 N N N N
vg0404379553 C -> A LOC_Os04g08210-LOC_Os04g08230 intergenic_region ; MODIFIER N Average:41.636; most accessible tissue: Zhenshan97 flag leaf, score: 71.238 N N N N
vg0404379553 C -> T LOC_Os04g08210-LOC_Os04g08230 intergenic_region ; MODIFIER silent_mutation Average:41.636; most accessible tissue: Zhenshan97 flag leaf, score: 71.238 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0404379553 NA 1.89E-06 mr1715 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
vg0404379553 NA 6.62E-06 mr1036_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
vg0404379553 NA 6.94E-10 mr1062_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
vg0404379553 NA 5.50E-06 mr1265_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
vg0404379553 NA 3.48E-06 mr1360_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
vg0404379553 NA 2.39E-06 mr1527_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
vg0404379553 NA 2.86E-06 mr1659_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
vg0404379553 NA 1.80E-12 mr1715_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
vg0404379553 NA 4.70E-08 mr1758_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
vg0404379553 NA 1.64E-07 mr1842_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
vg0404379553 NA 8.09E-07 mr1895_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
vg0404379553 NA 2.70E-09 mr1902_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