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Detailed information for vg0409515151:

Variant ID: vg0409515151 (JBrowse)Variation Type: INDEL
Chromosome: chr04Position: 9515151
Reference Allele: TAAlternative Allele: AA,T
Primary Allele: TASecondary Allele: AA

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACACATCGGCTGTCATGCATCAGCAACACTAGCCGATCATGCGTCAACCCAAACACTTGGGTAATACTTCTTCAAGTATTTGCCATTGAGCGCCCATCCA[TA/AA,T]
AACCTCACCATCAAGCCCTTGCAACATATATGCCCCTTTAGACACAACATTATAGATTTGAAACGGTCCTTCCCAATTTGGTGACCACTTGCCGAACTTG

Reverse complement sequence

CAAGTTCGGCAAGTGGTCACCAAATTGGGAAGGACCGTTTCAAATCTATAATGTTGTGTCTAAAGGGGCATATATGTTGCAAGGGCTTGATGGTGAGGTT[TA/TT,A]
TGGATGGGCGCTCAATGGCAAATACTTGAAGAAGTATTACCCAAGTGTTTGGGTTGACGCATGATCGGCTAGTGTTGCTGATGCATGACAGCCGATGTGT

Allele Frequencies:

Populations Population SizeFrequency of TA(primary allele) Frequency of AA(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 63.10% 26.30% 1.21% 9.39% NA
All Indica  2759 61.20% 38.70% 0.14% 0.00% NA
All Japonica  1512 70.60% 1.10% 0.73% 27.51% NA
Aus  269 52.80% 47.20% 0.00% 0.00% NA
Indica I  595 76.80% 23.20% 0.00% 0.00% NA
Indica II  465 49.50% 49.90% 0.65% 0.00% NA
Indica III  913 64.10% 35.90% 0.00% 0.00% NA
Indica Intermediate  786 52.90% 46.90% 0.13% 0.00% NA
Temperate Japonica  767 97.80% 0.40% 0.26% 1.56% NA
Tropical Japonica  504 26.60% 1.40% 1.39% 70.63% NA
Japonica Intermediate  241 76.30% 2.90% 0.83% 19.92% NA
VI/Aromatic  96 31.20% 5.20% 38.54% 25.00% NA
Intermediate  90 58.90% 31.10% 5.56% 4.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0409515151 TA -> DEL LOC_Os04g17380.1 N frameshift_variant Average:35.779; most accessible tissue: Minghui63 young leaf, score: 61.007 N N N N
vg0409515151 TA -> AA LOC_Os04g17380.1 missense_variant ; p.Tyr152Phe; MODERATE nonsynonymous_codon ; Y152F Average:35.779; most accessible tissue: Minghui63 young leaf, score: 61.007 benign +0.293 N N
vg0409515151 TA -> T LOC_Os04g17380.1 frameshift_variant ; p.Tyr152fs; HIGH N Average:35.779; most accessible tissue: Minghui63 young leaf, score: 61.007 N N N N
vg0409515151 TA -> T LOC_Os04g17370.1 downstream_gene_variant ; 473.0bp to feature; MODIFIER N Average:35.779; most accessible tissue: Minghui63 young leaf, score: 61.007 N N N N
vg0409515151 TA -> T LOC_Os04g17390.1 downstream_gene_variant ; 1327.0bp to feature; MODIFIER N Average:35.779; most accessible tissue: Minghui63 young leaf, score: 61.007 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0409515151 NA 1.57E-06 mr1062 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
vg0409515151 NA 1.49E-06 mr1403 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
vg0409515151 NA 8.91E-07 mr1414 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
vg0409515151 NA 8.08E-08 mr1830 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
vg0409515151 7.97E-06 1.10E-16 mr1846 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
vg0409515151 NA 8.89E-13 mr1846 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
vg0409515151 NA 5.04E-07 mr1317_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
vg0409515151 NA 7.38E-07 mr1608_2 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
vg0409515151 NA 8.70E-07 mr1608_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
vg0409515151 NA 3.31E-07 mr1818_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
vg0409515151 NA 3.33E-12 mr1830_2 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
vg0409515151 NA 4.55E-10 mr1830_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
vg0409515151 NA 6.65E-25 mr1846_2 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
vg0409515151 NA 8.39E-22 mr1846_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