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Detailed information for vg0407628826:

Variant ID: vg0407628826 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 7628826
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.84, T: 0.16, others allele: 0.00, population size: 76. )

Flanking Sequence (100 bp) in Reference Genome:


GTGCTACCGGTGGTCCTATAGGAAATCAAGGCGATAACCCTCAAGAAGTGCACGGAGCTCCAAGTGATGTTGCTCAAGGGCTGCAAGGAGGAAATCTTAA[C/T]
CAGAATATTGAGCTAGCACAAGATTTTTTCAACAACTTTCAGGATCGGGTTGATTACGCGGTGCATCATGCTTTGATCAATCAATCCGGGGTCTTAGTCA

Reverse complement sequence

TGACTAAGACCCCGGATTGATTGATCAAAGCATGATGCACCGCGTAATCAACCCGATCCTGAAAGTTGTTGAAAAAATCTTGTGCTAGCTCAATATTCTG[G/A]
TTAAGATTTCCTCCTTGCAGCCCTTGAGCAACATCACTTGGAGCTCCGTGCACTTCTTGAGGGTTATCGCCTTGATTTCCTATAGGACCACCGGTAGCAC

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 35.60% 10.30% 5.54% 48.50% NA
All Indica  2759 3.50% 17.50% 8.30% 70.64% NA
All Japonica  1512 98.50% 0.10% 0.07% 1.39% NA
Aus  269 0.70% 0.00% 3.35% 95.91% NA
Indica I  595 2.70% 2.00% 4.87% 90.42% NA
Indica II  465 4.90% 29.20% 7.74% 58.06% NA
Indica III  913 2.00% 20.70% 9.97% 67.36% NA
Indica Intermediate  786 5.10% 18.70% 9.29% 66.92% NA
Temperate Japonica  767 99.50% 0.10% 0.00% 0.39% NA
Tropical Japonica  504 97.20% 0.00% 0.20% 2.58% NA
Japonica Intermediate  241 97.90% 0.00% 0.00% 2.07% NA
VI/Aromatic  96 52.10% 0.00% 19.79% 28.12% NA
Intermediate  90 51.10% 3.30% 4.44% 41.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0407628826 C -> DEL LOC_Os04g13660.1 N frameshift_variant Average:16.0; most accessible tissue: Minghui63 young leaf, score: 24.836 N N N N
vg0407628826 C -> T LOC_Os04g13660.1 synonymous_variant ; p.Asn141Asn; LOW synonymous_codon Average:16.0; most accessible tissue: Minghui63 young leaf, score: 24.836 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0407628826 NA 7.23E-07 mr1425 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
vg0407628826 4.39E-06 NA mr1425_2 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
vg0407628826 NA 1.03E-07 mr1425_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
vg0407628826 NA 3.15E-08 mr1446_2 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