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Detailed information for vg0414371844:

Variant ID: vg0414371844 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 14371844
Reference Allele: CAlternative Allele: A
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.93, A: 0.07, others allele: 0.00, population size: 81. )

Flanking Sequence (100 bp) in Reference Genome:


AGGGTAGCACTAGCTGCTGCATTGTTTACAACATAGCCAGACCTAGAAAGCCAACAGTACTAGAAAATGGTTTTTTTTAACTGTCAACGTTTTTTTATGG[C/A]
TAGGAAATTGCTTTCACTGAAAATGAACCTTTTGACATCTGGGAGCAATGCTTCACGAAAACTGCTCTTTTCGTGGAAGGAAGGATATTCCAGAAGTGAA

Reverse complement sequence

TTCACTTCTGGAATATCCTTCCTTCCACGAAAAGAGCAGTTTTCGTGAAGCATTGCTCCCAGATGTCAAAAGGTTCATTTTCAGTGAAAGCAATTTCCTA[G/T]
CCATAAAAAAACGTTGACAGTTAAAAAAAACCATTTTCTAGTACTGTTGGCTTTCTAGGTCTGGCTATGTTGTAAACAATGCAGCAGCTAGTGCTACCCT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 72.90% 21.80% 0.19% 5.14% NA
All Indica  2759 87.80% 7.90% 0.14% 4.20% NA
All Japonica  1512 41.50% 50.90% 0.26% 7.34% NA
Aus  269 98.90% 1.10% 0.00% 0.00% NA
Indica I  595 71.30% 15.10% 0.50% 13.11% NA
Indica II  465 95.70% 4.10% 0.00% 0.22% NA
Indica III  913 92.90% 5.80% 0.00% 1.31% NA
Indica Intermediate  786 89.70% 7.00% 0.13% 3.18% NA
Temperate Japonica  767 6.90% 84.70% 0.52% 7.82% NA
Tropical Japonica  504 86.50% 6.30% 0.00% 7.14% NA
Japonica Intermediate  241 57.30% 36.50% 0.00% 6.22% NA
VI/Aromatic  96 76.00% 12.50% 1.04% 10.42% NA
Intermediate  90 63.30% 30.00% 0.00% 6.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0414371844 C -> DEL N N silent_mutation Average:20.238; most accessible tissue: Callus, score: 42.552 N N N N
vg0414371844 C -> A LOC_Os04g24950.1 intron_variant ; MODIFIER silent_mutation Average:20.238; most accessible tissue: Callus, score: 42.552 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0414371844 NA 3.86E-07 mr1295 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
vg0414371844 NA 1.63E-06 mr1330 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
vg0414371844 NA 2.38E-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
vg0414371844 NA 2.41E-06 mr1548 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
vg0414371844 NA 1.48E-07 mr1579 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
vg0414371844 3.39E-07 3.39E-07 mr1621 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
vg0414371844 7.11E-06 7.11E-06 mr1701 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
vg0414371844 7.37E-06 7.37E-06 mr1779 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