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Detailed information for vg0821373981:

Variant ID: vg0821373981 (JBrowse)Variation Type: INDEL
Chromosome: chr08Position: 21373981
Reference Allele: GAlternative Allele: T,GGAA
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 322. )

Flanking Sequence (100 bp) in Reference Genome:


TGTGAATAGGACAATAGACATCACGAGTTGGAGAAGTACGCTGAATTCCACGCTCTTTGCAGGCACGAATTTCAGCGTGGACGTTGAGAAAAACCCAACA[G/T,GGAA]
GCTTGCAAGGTGTGTTTTCTGGTTTTGTGGATAGGACACCAGGACCTTGTCACCTCGGAAGTCATCCTCGTCGGCTCGTGATTCTTGTCGGAAAGGCAAG

Reverse complement sequence

CTTGCCTTTCCGACAAGAATCACGAGCCGACGAGGATGACTTCCGAGGTGACAAGGTCCTGGTGTCCTATCCACAAAACCAGAAAACACACCTTGCAAGC[C/A,TTCC]
TGTTGGGTTTTTCTCAACGTCCACGCTGAAATTCGTGCCTGCAAAGAGCGTGGAATTCAGCGTACTTCTCCAACTCGTGATGTCTATTGTCCTATTCACA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 89.50% 10.50% 0.02% 0.00% NA
All Indica  2759 99.70% 0.30% 0.00% 0.00% NA
All Japonica  1512 68.60% 31.30% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.20% 0.80% 0.00% 0.00% NA
Temperate Japonica  767 97.30% 2.70% 0.00% 0.00% NA
Tropical Japonica  504 28.00% 71.80% 0.20% 0.00% NA
Japonica Intermediate  241 62.20% 37.80% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 83.30% 16.70% 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
vg0821373981 G -> GGAA LOC_Os08g34090.1 disruptive_inframe_insertion ; p.Ala164_Cys165insSer; MODERATE N Average:55.667; most accessible tissue: Zhenshan97 flower, score: 73.946 N N N N
vg0821373981 G -> T LOC_Os08g34090.1 synonymous_variant ; p.Ala164Ala; LOW synonymous_codon Average:55.667; most accessible tissue: Zhenshan97 flower, score: 73.946 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0821373981 NA 4.60E-10 mr1017 Jap_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
vg0821373981 NA 5.77E-07 mr1364 Jap_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
vg0821373981 1.01E-06 1.17E-08 mr1388 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
vg0821373981 1.12E-06 3.08E-07 mr1388 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
vg0821373981 NA 2.16E-07 mr1443 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
vg0821373981 NA 6.31E-07 mr1443 Jap_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
vg0821373981 NA 1.34E-07 mr1510 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
vg0821373981 NA 3.78E-09 mr1533 Jap_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
vg0821373981 NA 2.55E-10 mr1554 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
vg0821373981 NA 4.65E-08 mr1602 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
vg0821373981 NA 3.78E-11 mr1980 Jap_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