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Detailed information for vg0700231073:

Variant ID: vg0700231073 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 231073
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCAGCATATTCTAGTTAATCATAACTAAGCTTTTCTTCATTATCATCATCAGATTCATTAATATCAAAACTTGCATTACGAGCAATAAAAGCTAGATCAA[C/T]
AACTTGCTTACCTTTGCTCTCATCTTCATCTTCCGATTCATCAAAAACTTTTATGAGTTCTTGGATTAACCACTGCATACAATGCTTCTTCTTCTCCTTC

Reverse complement sequence

GAAGGAGAAGAAGAAGCATTGTATGCAGTGGTTAATCCAAGAACTCATAAAAGTTTTTGATGAATCGGAAGATGAAGATGAGAGCAAAGGTAAGCAAGTT[G/A]
TTGATCTAGCTTTTATTGCTCGTAATGCAAGTTTTGATATTAATGAATCTGATGATGATAATGAAGAAAAGCTTAGTTATGATTAACTAGAATATGCTGC

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 98.70% 1.10% 0.15% 0.00% NA
All Indica  2759 97.90% 1.80% 0.25% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 92.70% 6.20% 1.08% 0.00% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 97.30% 2.40% 0.25% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 0.00% 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
vg0700231073 C -> T LOC_Os07g01370.1 upstream_gene_variant ; 4830.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0700231073 C -> T LOC_Os07g01350.1 downstream_gene_variant ; 4695.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0700231073 C -> T LOC_Os07g01360.1 intron_variant ; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0700231073 2.00E-06 1.96E-09 mr1829 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
vg0700231073 NA 1.02E-07 mr1902 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
vg0700231073 NA 9.88E-06 mr1944 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