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Detailed information for vg1011837474:

Variant ID: vg1011837474 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 11837474
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGAGTGCTACGTCTAGCCATCTCCCTGTCGAACGCAACTCATCGAAAGGCCCGGGACACCCGGCCCAGAGTGTTCGATTCCACCGATCGAGAACGCCGAT[C/T]
GCCTCCAGCTTCAATCAACCCGAGCGTGCGGCCGCACGTCTCCCTGTCGAGAGTAGCTCACTGGAAAGTTCGAGCCACCCGCCCGAAGTGTCCAACCCAC

Reverse complement sequence

GTGGGTTGGACACTTCGGGCGGGTGGCTCGAACTTTCCAGTGAGCTACTCTCGACAGGGAGACGTGCGGCCGCACGCTCGGGTTGATTGAAGCTGGAGGC[G/A]
ATCGGCGTTCTCGATCGGTGGAATCGAACACTCTGGGCCGGGTGTCCCGGGCCTTTCGATGAGTTGCGTTCGACAGGGAGATGGCTAGACGTAGCACTCG

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 96.80% 1.20% 1.97% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 90.10% 3.80% 6.08% 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 80.70% 7.40% 11.86% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.00% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 96.70% 2.20% 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
vg1011837474 C -> T LOC_Os10g22780.1 upstream_gene_variant ; 3663.0bp to feature; MODIFIER silent_mutation Average:58.52; most accessible tissue: Minghui63 young leaf, score: 78.054 N N N N
vg1011837474 C -> T LOC_Os10g22770.1 intron_variant ; MODIFIER silent_mutation Average:58.52; most accessible tissue: Minghui63 young leaf, score: 78.054 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1011837474 NA 4.64E-06 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
vg1011837474 NA 4.19E-08 mr1757 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
vg1011837474 NA 7.85E-07 mr1902 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
vg1011837474 NA 2.63E-06 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
vg1011837474 8.25E-07 6.46E-09 mr1549_2 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
vg1011837474 9.27E-06 8.88E-08 mr1757_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
vg1011837474 NA 7.97E-06 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