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Detailed information for vg0427340146:

Variant ID: vg0427340146 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 27340146
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCCACGGGCGGGCTGATGAACAAGATGACCGGGCGCATCGGCGACTCGCCGTTGATCGGGTCGGGGGAAGGCAAGGGCATCATACGCTCCACGCTGGCGC[G/A]
CGACGTCGCCGCCGTGATGGAGTTCAGGGGCGCCGGGCTGCAGGAGGCCATCGACTACTGCGTCAAGGAACGGCTGGACGAAGGGCTCATCGGGCTCATC

Reverse complement sequence

GATGAGCCCGATGAGCCCTTCGTCCAGCCGTTCCTTGACGCAGTAGTCGATGGCCTCCTGCAGCCCGGCGCCCCTGAACTCCATCACGGCGGCGACGTCG[C/T]
GCGCCAGCGTGGAGCGTATGATGCCCTTGCCTTCCCCCGACCCGATCAACGGCGAGTCGCCGATGCGCCCGGTCATCTTGTTCATCAGCCCGCCCGTGGA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 95.70% 0.40% 3.45% 0.42% NA
All Indica  2759 93.80% 0.70% 5.40% 0.04% NA
All Japonica  1512 97.90% 0.00% 0.79% 1.26% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 83.70% 1.30% 14.96% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 94.90% 0.90% 4.27% 0.00% NA
Indica Intermediate  786 96.70% 0.50% 2.67% 0.13% NA
Temperate Japonica  767 99.90% 0.00% 0.00% 0.13% NA
Tropical Japonica  504 94.80% 0.00% 2.38% 2.78% NA
Japonica Intermediate  241 98.30% 0.00% 0.00% 1.66% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 0.00% 2.22% 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
vg0427340146 G -> DEL LOC_Os04g46150.1 N frameshift_variant Average:42.475; most accessible tissue: Minghui63 panicle, score: 59.629 N N N N
vg0427340146 G -> A LOC_Os04g46150.1 missense_variant ; p.Arg35His; MODERATE nonsynonymous_codon ; R35H Average:42.475; most accessible tissue: Minghui63 panicle, score: 59.629 probably damaging 2.48 TOLERATED 0.24

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0427340146 1.44E-07 1.02E-06 mr1745 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
vg0427340146 4.48E-09 1.47E-08 mr1745_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