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Detailed information for vg1013502705:

Variant ID: vg1013502705 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 13502705
Reference Allele: TAlternative Allele: C,A
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 381. )

Flanking Sequence (100 bp) in Reference Genome:


AGAGATGTGCCAAGCGCAACACTAAATACAAGGCGATGTTTCTCAATGTACCGGTGAACCCACATCCCCATTTCTAATGCTCCGAGCTGCGAACAAGCAG[T/C,A]
TAGAAGATTGACCATTGTGATCTCATCAGGCACCACACTTGCTTCCTGCATCTCATGAAACAAGGAAAGGGCCTCCTTGCACTGCTTACACTGCACATAA

Reverse complement sequence

TTATGTGCAGTGTAAGCAGTGCAAGGAGGCCCTTTCCTTGTTTCATGAGATGCAGGAAGCAAGTGTGGTGCCTGATGAGATCACAATGGTCAATCTTCTA[A/G,T]
CTGCTTGTTCGCAGCTCGGAGCATTAGAAATGGGGATGTGGGTTCACCGGTACATTGAGAAACATCGCCTTGTATTTAGTGTTGCGCTTGGCACATCTCT

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 91.50% 8.50% 0.00% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 74.20% 25.80% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.60% 0.40% 0.00% 0.00% NA
Temperate Japonica  767 94.70% 5.30% 0.00% 0.00% NA
Tropical Japonica  504 51.00% 49.00% 0.00% 0.00% NA
Japonica Intermediate  241 57.70% 42.30% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 91.10% 8.90% 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
vg1013502705 T -> C LOC_Os10g26070.1 missense_variant ; p.Thr368Ala; MODERATE nonsynonymous_codon ; T368A Average:65.111; most accessible tissue: Callus, score: 81.55 benign 0.688 DELETERIOUS 0.05
vg1013502705 T -> A LOC_Os10g26070.1 missense_variant ; p.Thr368Ser; MODERATE N Average:65.111; most accessible tissue: Callus, score: 81.55 N N N N
vg1013502705 T -> A LOC_Os10g26060.1 upstream_gene_variant ; 3270.0bp to feature; MODIFIER N Average:65.111; most accessible tissue: Callus, score: 81.55 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1013502705 NA 1.15E-06 mr1248 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
vg1013502705 NA 1.53E-18 mr1301 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
vg1013502705 3.91E-07 NA mr1533 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
vg1013502705 2.40E-06 3.55E-14 mr1533 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
vg1013502705 NA 1.32E-07 mr1668 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
vg1013502705 NA 1.76E-28 mr1699 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
vg1013502705 NA 1.85E-11 mr1871 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
vg1013502705 3.30E-11 NA mr1980 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
vg1013502705 1.38E-08 8.81E-22 mr1980 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
vg1013502705 NA 1.60E-14 mr1410_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
vg1013502705 9.45E-13 NA mr1533_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
vg1013502705 8.96E-11 2.47E-25 mr1533_2 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
vg1013502705 NA 3.39E-07 mr1819_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
vg1013502705 4.12E-07 NA mr1980_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
vg1013502705 NA 7.30E-10 mr1980_2 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