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Detailed information for vg1210160121:

Variant ID: vg1210160121 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 10160121
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GAGTTGCGACATGGCCCAAACTCGCGAGATGGCGTCTGCCCGAGAGGATATCCGACTGGCTGCAGCCACGGCAAGCGAAGGAGAAGTGCCCGCTACCAAG[A/G]
TTTCAAAGAGCGGAGAAAGCGAAGCCAAGACTAAGAAGATTCCCCTAGATCCCTCTGATCCTACTAAAACTGCTGTAATAGGCGCCGAGTTAGATTGTAA

Reverse complement sequence

TTACAATCTAACTCGGCGCCTATTACAGCAGTTTTAGTAGGATCAGAGGGATCTAGGGGAATCTTCTTAGTCTTGGCTTCGCTTTCTCCGCTCTTTGAAA[T/C]
CTTGGTAGCGGGCACTTCTCCTTCGCTTGCCGTGGCTGCAGCCAGTCGGATATCCTCTCGGGCAGACGCCATCTCGCGAGTTTGGGCCATGTCGCAACTC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 39.60% 0.70% 4.80% 54.82% NA
All Indica  2759 13.00% 1.20% 5.94% 79.85% NA
All Japonica  1512 78.60% 0.00% 2.25% 19.18% NA
Aus  269 76.60% 0.70% 5.20% 17.47% NA
Indica I  595 9.40% 0.00% 5.21% 85.38% NA
Indica II  465 17.20% 4.10% 5.16% 73.55% NA
Indica III  913 6.80% 0.30% 6.90% 85.98% NA
Indica Intermediate  786 20.50% 1.40% 5.85% 72.26% NA
Temperate Japonica  767 89.60% 0.00% 1.69% 8.74% NA
Tropical Japonica  504 65.30% 0.00% 1.79% 32.94% NA
Japonica Intermediate  241 71.40% 0.00% 4.98% 23.65% NA
VI/Aromatic  96 69.80% 0.00% 13.54% 16.67% NA
Intermediate  90 58.90% 0.00% 2.22% 38.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1210160121 A -> DEL LOC_Os12g17740.1 N frameshift_variant Average:23.398; most accessible tissue: Minghui63 flag leaf, score: 58.568 N N N N
vg1210160121 A -> G LOC_Os12g17740.1 missense_variant ; p.Ile942Val; MODERATE nonsynonymous_codon ; I942V Average:23.398; most accessible tissue: Minghui63 flag leaf, score: 58.568 benign 0.053 TOLERATED 0.39

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1210160121 1.49E-06 1.49E-06 mr1926 Ind_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
vg1210160121 NA 1.98E-07 mr1002_2 Ind_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