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Detailed information for vg1011836497:

Variant ID: vg1011836497 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 11836497
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGCTCTGCCGGATATATTAAAAAGAAGTAAAAGGAGTCAGACAAAACGAAAAACATCAAGCTTAGGACACCGCCAATGACAACGCTGCCGATGCTGCCAC[C/T]
GTAGGCTTCCCGCCGGTGAGGATGCTGACGACCACGGTAACGGCCTCCCCGACACAGGAGCGTCGCTGCCGCCCCTTCGCCGGTACTTGCCCCGACGACA

Reverse complement sequence

TGTCGTCGGGGCAAGTACCGGCGAAGGGGCGGCAGCGACGCTCCTGTGTCGGGGAGGCCGTTACCGTGGTCGTCAGCATCCTCACCGGCGGGAAGCCTAC[G/A]
GTGGCAGCATCGGCAGCGTTGTCATTGGCGGTGTCCTAAGCTTGATGTTTTTCGTTTTGTCTGACTCCTTTTACTTCTTTTTAATATATCCGGCAGAGCT

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 94.50% 4.40% 1.10% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 83.10% 13.50% 3.37% 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  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 67.40% 25.90% 6.65% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 98.30% 1.70% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 95.60% 3.30% 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
vg1011836497 C -> T LOC_Os10g22770.1 missense_variant ; p.Gly268Ser; MODERATE nonsynonymous_codon ; G268S Average:59.699; most accessible tissue: Callus, score: 81.488 unknown unknown DELETERIOUS 0.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1011836497 NA 8.72E-11 Heading_date Jap_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg1011836497 NA 1.66E-07 mr1354 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
vg1011836497 NA 4.38E-07 mr1829 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
vg1011836497 7.44E-06 9.99E-09 mr1902 Jap_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
vg1011836497 NA 1.00E-08 mr1354_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
vg1011836497 NA 6.76E-06 mr1829_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
vg1011836497 NA 6.40E-07 mr1902_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