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Detailed information for vg0102812041:

Variant ID: vg0102812041 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 2812041
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCAGCCTCAGGATGAACAGTCTCGAGGGCACAATACCTCCTGAATTCGGCAGCAACATGCCGCGCCTTTACTTCCTCGACATCTGCTCCAACAACCTGAG[T/C]
GGTGCACTCCCGTCTTCCCTGTACAATCTGTCGTCGCTAATGGGGTTTGATGCAGGAAACAACAAGCTGGATGGAAGCATTGCTACTGATATCGATGAAA

Reverse complement sequence

TTTCATCGATATCAGTAGCAATGCTTCCATCCAGCTTGTTGTTTCCTGCATCAAACCCCATTAGCGACGACAGATTGTACAGGGAAGACGGGAGTGCACC[A/G]
CTCAGGTTGTTGGAGCAGATGTCGAGGAAGTAAAGGCGCGGCATGTTGCTGCCGAATTCAGGAGGTATTGTGCCCTCGAGACTGTTCATCCTGAGGCTGA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 71.90% 27.40% 0.28% 0.51% NA
All Indica  2759 57.10% 41.70% 0.43% 0.76% NA
All Japonica  1512 92.30% 7.70% 0.00% 0.00% NA
Aus  269 97.80% 2.20% 0.00% 0.00% NA
Indica I  595 76.00% 23.40% 0.50% 0.17% NA
Indica II  465 30.50% 67.10% 1.08% 1.29% NA
Indica III  913 61.40% 37.60% 0.00% 0.99% NA
Indica Intermediate  786 53.40% 45.40% 0.51% 0.64% NA
Temperate Japonica  767 85.40% 14.60% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 1.20% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 74.40% 21.10% 1.11% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0102812041 T -> DEL LOC_Os01g05870.1 N frameshift_variant Average:69.833; most accessible tissue: Callus, score: 85.869 N N N N
vg0102812041 T -> C LOC_Os01g05870.1 synonymous_variant ; p.Ser234Ser; LOW synonymous_codon Average:69.833; most accessible tissue: Callus, score: 85.869 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0102812041 NA 1.74E-13 mr1174 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
vg0102812041 NA 8.45E-09 mr1174 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
vg0102812041 NA 1.19E-06 mr1347 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
vg0102812041 NA 1.11E-13 mr1174_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
vg0102812041 NA 4.12E-09 mr1174_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
vg0102812041 NA 8.28E-09 mr1347_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
vg0102812041 NA 5.16E-06 mr1419_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
vg0102812041 NA 5.11E-06 mr1420_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
vg0102812041 NA 3.66E-07 mr1604_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