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Detailed information for vg0618322026:

Variant ID: vg0618322026 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 18322026
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACGCCGAGTTCTCCTACAATAACAGCTACCAAGCCAGCATACAAATGGCACCCTATGAAGCGTTGTATGGACACAAATGCCGGACACCGCTATTGTGGGA[C/T]
CAAGTTGGGGAAAGCCAAGTGTTCAGGACCGATATCTTGAGAGAAGCTGAAGCGAAGGTCAGAACCATTCAGGATAATCTAAAGGTGGCACAGTCCCAGC

Reverse complement sequence

GCTGGGACTGTGCCACCTTTAGATTATCCTGAATGGTTCTGACCTTCGCTTCAGCTTCTCTCAAGATATCGGTCCTGAACACTTGGCTTTCCCCAACTTG[G/A]
TCCCACAATAGCGGTGTCCGGCATTTGTGTCCATACAACGCTTCATAGGGTGCCATTTGTATGCTGGCTTGGTAGCTGTTATTGTAGGAGAACTCGGCGT

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 61.60% 3.40% 1.95% 32.97% NA
All Indica  2759 52.60% 4.90% 2.39% 40.09% NA
All Japonica  1512 82.60% 0.00% 0.26% 17.13% NA
Aus  269 46.10% 9.30% 7.06% 37.55% NA
Indica I  595 53.80% 16.10% 2.86% 27.23% NA
Indica II  465 67.30% 0.20% 1.08% 31.40% NA
Indica III  913 41.50% 0.30% 2.30% 55.86% NA
Indica Intermediate  786 56.00% 4.50% 2.93% 36.64% NA
Temperate Japonica  767 76.70% 0.00% 0.13% 23.21% NA
Tropical Japonica  504 91.90% 0.00% 0.20% 7.94% NA
Japonica Intermediate  241 82.20% 0.00% 0.83% 17.01% NA
VI/Aromatic  96 30.20% 1.00% 2.08% 66.67% NA
Intermediate  90 65.60% 2.20% 1.11% 31.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0618322026 C -> T LOC_Os06g31480.1 synonymous_variant ; p.Asp1531Asp; LOW synonymous_codon Average:8.731; most accessible tissue: Callus, score: 28.865 N N N N
vg0618322026 C -> DEL LOC_Os06g31480.1 N frameshift_variant Average:8.731; most accessible tissue: Callus, score: 28.865 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0618322026 3.66E-06 NA mr1435 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