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Detailed information for vg0101141375:

Variant ID: vg0101141375 (JBrowse)Variation Type: INDEL
Chromosome: chr01Position: 1141375
Reference Allele: GTAlternative Allele: G,AT
Primary Allele: GTSecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TACGTGTTTGATTTTAGAAATGATATCACATGTTTTCCATGCGAGAGTTGAGAGAGAGAGAGAGAGTTATCAGAATTTGAGTATATCCATATGCAATAGT[GT/G,AT]
TTTTTTATCCGTTCTATGAGTATATCAATCATGCGCTAATATCTTTCTTTCTTTGTGCGTGTTAATTTTATCTTCATCTTCATTAAAAAAACACCAACTT

Reverse complement sequence

AAGTTGGTGTTTTTTTAATGAAGATGAAGATAAAATTAACACGCACAAAGAAAGAAAGATATTAGCGCATGATTGATATACTCATAGAACGGATAAAAAA[AC/C,AT]
ACTATTGCATATGGATATACTCAAATTCTGATAACTCTCTCTCTCTCTCTCAACTCTCGCATGGAAAACATGTGATATCATTTCTAAAATCAAACACGTA

Allele Frequencies:

Populations Population SizeFrequency of GT(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 56.90% 40.50% 0.80% 0.00% AT: 1.86%
All Indica  2759 46.80% 52.90% 0.25% 0.00% NA
All Japonica  1512 82.90% 9.50% 1.79% 0.00% AT: 5.82%
Aus  269 6.70% 93.30% 0.00% 0.00% NA
Indica I  595 34.60% 65.00% 0.34% 0.00% NA
Indica II  465 25.20% 74.20% 0.65% 0.00% NA
Indica III  913 67.40% 32.60% 0.00% 0.00% NA
Indica Intermediate  786 45.00% 54.70% 0.25% 0.00% NA
Temperate Japonica  767 81.90% 3.90% 3.00% 0.00% AT: 11.21%
Tropical Japonica  504 79.40% 20.00% 0.40% 0.00% AT: 0.20%
Japonica Intermediate  241 93.40% 5.40% 0.83% 0.00% AT: 0.41%
VI/Aromatic  96 78.10% 21.90% 0.00% 0.00% NA
Intermediate  90 54.40% 41.10% 4.44% 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
vg0101141375 GT -> G LOC_Os01g02990.1 upstream_gene_variant ; 3752.0bp to feature; MODIFIER silent_mutation Average:40.61; most accessible tissue: Callus, score: 57.985 N N N N
vg0101141375 GT -> G LOC_Os01g03010.1 downstream_gene_variant ; 2181.0bp to feature; MODIFIER silent_mutation Average:40.61; most accessible tissue: Callus, score: 57.985 N N N N
vg0101141375 GT -> G LOC_Os01g03020.1 downstream_gene_variant ; 4453.0bp to feature; MODIFIER silent_mutation Average:40.61; most accessible tissue: Callus, score: 57.985 N N N N
vg0101141375 GT -> G LOC_Os01g02990-LOC_Os01g03010 intergenic_region ; MODIFIER silent_mutation Average:40.61; most accessible tissue: Callus, score: 57.985 N N N N
vg0101141375 GT -> AT LOC_Os01g02990.1 upstream_gene_variant ; 3751.0bp to feature; MODIFIER silent_mutation Average:40.61; most accessible tissue: Callus, score: 57.985 N N N N
vg0101141375 GT -> AT LOC_Os01g03010.1 downstream_gene_variant ; 2182.0bp to feature; MODIFIER silent_mutation Average:40.61; most accessible tissue: Callus, score: 57.985 N N N N
vg0101141375 GT -> AT LOC_Os01g03020.1 downstream_gene_variant ; 4454.0bp to feature; MODIFIER silent_mutation Average:40.61; most accessible tissue: Callus, score: 57.985 N N N N
vg0101141375 GT -> AT LOC_Os01g02990-LOC_Os01g03010 intergenic_region ; MODIFIER silent_mutation Average:40.61; most accessible tissue: Callus, score: 57.985 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0101141375 1.21E-06 1.21E-06 mr1499_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