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Detailed information for vg0501379198:

Variant ID: vg0501379198 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 1379198
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGGTGGGGTCTGGGCTCGTGAGGACGCGAGCCGTGAGAGTTCGTCGGCAATCATGTTATCCCGTCTGGGCACATGCCGAAGCTCGACCCCGTCGAAATGA[C/T]
GCTCCATACGCCGTATTTGGCGTACGTAAGCCTCCATCTGCGGGTCAGAGCACCGGTACTCCTTACAGACTTGGTTAACGACCAGCTGGGAGTCGCCTAA

Reverse complement sequence

TTAGGCGACTCCCAGCTGGTCGTTAACCAAGTCTGTAAGGAGTACCGGTGCTCTGACCCGCAGATGGAGGCTTACGTACGCCAAATACGGCGTATGGAGC[G/A]
TCATTTCGACGGGGTCGAGCTTCGGCATGTGCCCAGACGGGATAACATGATTGCCGACGAACTCTCACGGCTCGCGTCCTCACGAGCCCAGACCCCACCG

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 95.00% 4.70% 0.30% 0.00% NA
All Indica  2759 98.40% 1.20% 0.40% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.07% 0.00% NA
Aus  269 33.10% 66.20% 0.74% 0.00% NA
Indica I  595 98.80% 0.80% 0.34% 0.00% NA
Indica II  465 99.60% 0.20% 0.22% 0.00% NA
Indica III  913 98.50% 1.40% 0.11% 0.00% NA
Indica Intermediate  786 97.30% 1.80% 0.89% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.00% 0.41% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 92.20% 7.80% 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
vg0501379198 C -> T LOC_Os05g03360.1 missense_variant ; p.Arg1534His; MODERATE nonsynonymous_codon ; R1534H Average:38.928; most accessible tissue: Minghui63 young leaf, score: 65.161 benign 0.862 DELETERIOUS 0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0501379198 NA 1.82E-15 mr1113 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
vg0501379198 1.06E-07 2.46E-21 mr1114 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
vg0501379198 NA 3.52E-24 mr1123 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
vg0501379198 6.55E-09 7.44E-22 mr1242 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
vg0501379198 NA 1.06E-08 mr1348 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
vg0501379198 NA 7.64E-07 mr1415 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
vg0501379198 3.98E-06 1.77E-16 mr1496 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
vg0501379198 NA 7.64E-07 mr1567 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
vg0501379198 NA 5.46E-06 mr1621 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
vg0501379198 NA 7.93E-07 mr1931 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