Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923).

Detailed information for vg0128962067:

Variant ID: vg0128962067 (JBrowse)Variation Type: INDEL
Chromosome: chr01Position: 28962067
Reference Allele: CAlternative Allele: CTCTCTA,CTCTCTCTA,CTCTA
Primary Allele: CTCTCTASecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 104. )

Flanking Sequence (100 bp) in Reference Genome:


TCTCTCTCGAGACCGAGAGACCCACGTCTTTATCTCTCGATCTCTATATGTTCGCTAGTTCTCCCTCGATCCTCTTTCTCTTCACTCACTCACTCTCTCT[C/CTCTCTA,CTCTCTCTA,CTCTA]
TCTCTCTAGCAAAGGCTGGCCAAGAGAAGTGGTAGCTGGGCGGGGTCGGTGGTGGCTGGGCGGGAGAAGCGGCGGCGGCTGAGCGGGAGAAGAAGCATCG

Reverse complement sequence

CGATGCTTCTTCTCCCGCTCAGCCGCCGCCGCTTCTCCCGCCCAGCCACCACCGACCCCGCCCAGCTACCACTTCTCTTGGCCAGCCTTTGCTAGAGAGA[G/TAGAGAG,TAGAGAGAG,TAGAG]
AGAGAGAGTGAGTGAGTGAAGAGAAAGAGGATCGAGGGAGAACTAGCGAACATATAGAGATCGAGAGATAAAGACGTGGGTCTCTCGGTCTCGAGAGAGA

Allele Frequencies:

Populations Population SizeFrequency of CTCTCTA(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 57.50% 38.50% 3.91% 0.00% CTCTCTCTA: 0.08%; CTCTA: 0.02%
All Indica  2759 81.20% 13.10% 5.55% 0.00% CTCTCTCTA: 0.14%; CTCTA: 0.04%
All Japonica  1512 9.50% 89.90% 0.66% 0.00% NA
Aus  269 83.30% 10.40% 6.32% 0.00% NA
Indica I  595 85.00% 8.40% 6.55% 0.00% NA
Indica II  465 87.50% 6.20% 6.24% 0.00% NA
Indica III  913 76.90% 18.30% 4.27% 0.00% CTCTCTCTA: 0.44%; CTCTA: 0.11%
Indica Intermediate  786 79.40% 14.80% 5.85% 0.00% NA
Temperate Japonica  767 0.10% 99.70% 0.13% 0.00% NA
Tropical Japonica  504 26.60% 71.80% 1.59% 0.00% NA
Japonica Intermediate  241 3.30% 96.30% 0.41% 0.00% NA
VI/Aromatic  96 75.00% 21.90% 3.12% 0.00% NA
Intermediate  90 44.40% 53.30% 2.22% 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
vg0128962067 C -> CTCTCTCTA LOC_Os01g50440-LOC_Os01g50450 intergenic_region ; MODIFIER silent_mutation Average:70.306; most accessible tissue: Minghui63 young leaf, score: 80.883 N N N N
vg0128962067 C -> CTCTA LOC_Os01g50440-LOC_Os01g50450 intergenic_region ; MODIFIER silent_mutation Average:70.306; most accessible tissue: Minghui63 young leaf, score: 80.883 N N N N
vg0128962067 C -> CTCTCTA LOC_Os01g50440-LOC_Os01g50450 intergenic_region ; MODIFIER silent_mutation Average:70.306; most accessible tissue: Minghui63 young leaf, score: 80.883 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0128962067 NA 2.64E-08 mr1248 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
vg0128962067 NA 5.16E-06 mr1445 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
vg0128962067 NA 2.06E-09 mr1232_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
vg0128962067 NA 1.78E-06 mr1250_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
vg0128962067 3.80E-06 1.64E-06 mr1263_2 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
vg0128962067 NA 4.91E-06 mr1511_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
vg0128962067 NA 6.56E-06 mr1624_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
vg0128962067 NA 7.98E-10 mr1681_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
vg0128962067 NA 5.64E-18 mr1682_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
vg0128962067 NA 8.85E-06 mr1959_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