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Detailed information for vg0228442970:

Variant ID: vg0228442970 (JBrowse)Variation Type: INDEL
Chromosome: chr02Position: 28442970
Reference Allele: TAlternative Allele: G,TCTAG,TCTATCTATCTATCTATCTATC,TCTATC,TCTATCTATCTATC
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTCAATCCGGACTCCACATGCGCTCCTGCATGCTCTTCCTTCGTGAAGAAAAACAATCAATTAGATTTCTACGAGTATCATCTATCTATCTATCTATCTA[T/G,TCTAG,TCTATCTATCTATCTATCTATC,TCTATC,TCTATCTATCTATC]
TATATTATTAAAACAGCCTTAAAAGAAGACATCATGTTCGCTGTAGGGCTATAAATTCTCACATTAATCAGAGAAAAAGAAAAGAAGAGTCCAATTAGAA

Reverse complement sequence

TTCTAATTGGACTCTTCTTTTCTTTTTCTCTGATTAATGTGAGAATTTATAGCCCTACAGCGAACATGATGTCTTCTTTTAAGGCTGTTTTAATAATATA[A/C,CTAGA,GATAGATAGATAGATAGATAGA,GATAGA,GATAGATAGATAGA]
TAGATAGATAGATAGATAGATGATACTCGTAGAAATCTAATTGATTGTTTTTCTTCACGAAGGAAGAGCATGCAGGAGCGCATGTGGAGTCCGGATTGAG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 95.40% 4.30% 0.23% 0.00% TCTAG: 0.06%; TCTATC: 0.02%
All Indica  2759 96.70% 3.30% 0.04% 0.00% TCTATC: 0.04%
All Japonica  1512 92.90% 6.30% 0.66% 0.00% TCTAG: 0.13%
Aus  269 95.50% 4.10% 0.00% 0.00% TCTAG: 0.37%
Indica I  595 99.70% 0.20% 0.17% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 92.10% 7.90% 0.00% 0.00% NA
Indica Intermediate  786 97.80% 2.00% 0.00% 0.00% TCTATC: 0.13%
Temperate Japonica  767 93.60% 5.20% 0.91% 0.00% TCTAG: 0.26%
Tropical Japonica  504 95.60% 4.20% 0.20% 0.00% NA
Japonica Intermediate  241 85.10% 14.10% 0.83% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 94.40% 5.60% 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
vg0228442970 T -> TCTATCTATCTATC LOC_Os02g46610-LOC_Os02g46620 intergenic_region ; MODIFIER N Average:49.66; most accessible tissue: Callus, score: 68.922 N N N N
vg0228442970 T -> TCTAG LOC_Os02g46610-LOC_Os02g46620 intergenic_region ; MODIFIER silent_mutation Average:49.66; most accessible tissue: Callus, score: 68.922 N N N N
vg0228442970 T -> G LOC_Os02g46610-LOC_Os02g46620 intergenic_region ; MODIFIER silent_mutation Average:49.66; most accessible tissue: Callus, score: 68.922 N N N N
vg0228442970 T -> TCTATCTATCTATCTATCTATC LOC_Os02g46610-LOC_Os02g46620 intergenic_region ; MODIFIER N Average:49.66; most accessible tissue: Callus, score: 68.922 N N N N
vg0228442970 T -> TCTATC LOC_Os02g46610-LOC_Os02g46620 intergenic_region ; MODIFIER silent_mutation Average:49.66; most accessible tissue: Callus, score: 68.922 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0228442970 4.84E-07 9.51E-08 mr1219 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
vg0228442970 NA 9.34E-07 mr1201_2 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
vg0228442970 8.00E-07 6.78E-08 mr1219_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