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Detailed information for vg1023170552:

Variant ID: vg1023170552 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 23170552
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.98, C: 0.02, others allele: 0.00, population size: 204. )

Flanking Sequence (100 bp) in Reference Genome:


CCCCGACTGATAGCCGAGTCCCTCACCTCCGATCTCATGATTATCATCAGCCAAGCCTCAGCATCATCGGCACAGGATCTAGTCGCAGGAGCAGGGGTCA[T/C]
GACGAACGATCTATTCACTCGCCTCCCGAACGTCACAGGGAGCGCCGAGTCGAACGGCCTCGCTCTCCACCTCACCAGCGTCCCGTCGACCTTCGCGACA

Reverse complement sequence

TGTCGCGAAGGTCGACGGGACGCTGGTGAGGTGGAGAGCGAGGCCGTTCGACTCGGCGCTCCCTGTGACGTTCGGGAGGCGAGTGAATAGATCGTTCGTC[A/G]
TGACCCCTGCTCCTGCGACTAGATCCTGTGCCGATGATGCTGAGGCTTGGCTGATGATAATCATGAGATCGGAGGTGAGGGACTCGGCTATCAGTCGGGG

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 99.80% 0.10% 0.02% 0.00% NA
All Indica  2759 99.80% 0.20% 0.00% 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  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.70% 0.30% 0.00% 0.00% NA
Indica Intermediate  786 99.70% 0.30% 0.00% 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  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 1.10% 1.11% 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
vg1023170552 T -> C LOC_Os10g42999.1 synonymous_variant ; p.His356His; LOW N Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg1023170552 T -> C LOC_Os10g42980.1 upstream_gene_variant ; 3254.0bp to feature; MODIFIER N 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
vg1023170552 2.34E-06 NA mr1288 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
vg1023170552 9.10E-06 9.08E-06 mr1481 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