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Detailed information for vg0707975245:

Variant ID: vg0707975245 (JBrowse)Variation Type: INDEL
Chromosome: chr07Position: 7975245
Reference Allele: TAlternative Allele: TCA,A
Primary Allele: TSecondary Allele: TCA

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGACTCATTCAAGTTTCTGTGGGTCAAATGAAGTGAATTATCCTAATGCTTTACAAACAAATATTATACACAATTTCCTAGCTTCCTATTTATTTTAAAA[T/TCA,A]
CACTCTAGCTCCTATATAAACTTGTTAATTTCACCTTACCTAGCTTCCTATTTATTTTAAAATCGCTGCCTCGCTGACTGGTATATTCTTTTTATGTATA

Reverse complement sequence

TATACATAAAAAGAATATACCAGTCAGCGAGGCAGCGATTTTAAAATAAATAGGAAGCTAGGTAAGGTGAAATTAACAAGTTTATATAGGAGCTAGAGTG[A/TGA,T]
TTTTAAAATAAATAGGAAGCTAGGAAATTGTGTATAATATTTGTTTGTAAAGCATTAGGATAATTCACTTCATTTGACCCACAGAAACTTGAATGAGTCT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of TCA(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 91.10% 2.40% 2.33% 4.00% A: 0.19%
All Indica  2759 99.50% 0.00% 0.36% 0.11% NA
All Japonica  1512 73.60% 7.50% 6.35% 11.90% A: 0.60%
Aus  269 99.60% 0.00% 0.37% 0.00% NA
Indica I  595 99.70% 0.00% 0.34% 0.00% NA
Indica II  465 98.30% 0.00% 1.29% 0.43% NA
Indica III  913 99.90% 0.00% 0.11% 0.00% NA
Indica Intermediate  786 99.70% 0.00% 0.13% 0.13% NA
Temperate Japonica  767 84.70% 14.30% 0.39% 0.39% A: 0.13%
Tropical Japonica  504 45.60% 0.00% 17.86% 34.92% A: 1.59%
Japonica Intermediate  241 96.70% 1.70% 1.24% 0.41% NA
VI/Aromatic  96 99.00% 0.00% 0.00% 1.04% NA
Intermediate  90 91.10% 0.00% 3.33% 5.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0707975245 T -> DEL N N silent_mutation Average:54.262; most accessible tissue: Callus, score: 76.476 N N N N
vg0707975245 T -> TCA LOC_Os07g13940.1 upstream_gene_variant ; 4834.0bp to feature; MODIFIER silent_mutation Average:54.262; most accessible tissue: Callus, score: 76.476 N N N N
vg0707975245 T -> TCA LOC_Os07g13960.1 upstream_gene_variant ; 2672.0bp to feature; MODIFIER silent_mutation Average:54.262; most accessible tissue: Callus, score: 76.476 N N N N
vg0707975245 T -> TCA LOC_Os07g13950.1 intron_variant ; MODIFIER silent_mutation Average:54.262; most accessible tissue: Callus, score: 76.476 N N N N
vg0707975245 T -> A LOC_Os07g13940.1 upstream_gene_variant ; 4833.0bp to feature; MODIFIER silent_mutation Average:54.262; most accessible tissue: Callus, score: 76.476 N N N N
vg0707975245 T -> A LOC_Os07g13960.1 upstream_gene_variant ; 2673.0bp to feature; MODIFIER silent_mutation Average:54.262; most accessible tissue: Callus, score: 76.476 N N N N
vg0707975245 T -> A LOC_Os07g13950.1 intron_variant ; MODIFIER silent_mutation Average:54.262; most accessible tissue: Callus, score: 76.476 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0707975245 1.41E-07 4.70E-07 mr1068_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
vg0707975245 NA 5.25E-06 mr1094_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
vg0707975245 4.37E-06 4.37E-06 mr1111_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
vg0707975245 NA 7.13E-06 mr1211_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