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Detailed information for vg0605572207:

Variant ID: vg0605572207 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 5572207
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCCGCCGCAACAGCCTATCTTACCCCCACGTTCGACACCATCCCCCTTAATGTGCCCAACTCTGTCGCCACTGCTACAAGCAACTCCTAGCGCACCACCA[T/C]
TGTCGTCTCCAACAATAGAATTTCCCTACATCGCTGGCCTCGGGGATTCAAGATTAGAAAACTAGGCTTTTTCCTTTACAAGCCTCATCCCAACATATAA

Reverse complement sequence

TTATATGTTGGGATGAGGCTTGTAAAGGAAAAAGCCTAGTTTTCTAATCTTGAATCCCCGAGGCCAGCGATGTAGGGAAATTCTATTGTTGGAGACGACA[A/G]
TGGTGGTGCGCTAGGAGTTGCTTGTAGCAGTGGCGACAGAGTTGGGCACATTAAGGGGGATGGTGTCGAACGTGGGGGTAAGATAGGCTGTTGCGGCGGC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 96.70% 1.50% 1.82% 0.00% NA
All Indica  2759 99.50% 0.00% 0.54% 0.00% NA
All Japonica  1512 90.70% 4.60% 4.63% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 98.80% 0.00% 1.18% 0.00% NA
Indica II  465 99.40% 0.00% 0.65% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.40% 0.00% 0.64% 0.00% NA
Temperate Japonica  767 83.60% 7.30% 9.13% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 94.20% 5.80% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 0.00% 1.11% 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
vg0605572207 T -> C LOC_Os06g10680.1 upstream_gene_variant ; 392.0bp to feature; MODIFIER silent_mutation Average:60.836; most accessible tissue: Zhenshan97 young leaf, score: 80.589 N N N N
vg0605572207 T -> C LOC_Os06g10670.1 downstream_gene_variant ; 736.0bp to feature; MODIFIER silent_mutation Average:60.836; most accessible tissue: Zhenshan97 young leaf, score: 80.589 N N N N
vg0605572207 T -> C LOC_Os06g10690.1 downstream_gene_variant ; 3660.0bp to feature; MODIFIER silent_mutation Average:60.836; most accessible tissue: Zhenshan97 young leaf, score: 80.589 N N N N
vg0605572207 T -> C LOC_Os06g10690.2 downstream_gene_variant ; 3660.0bp to feature; MODIFIER silent_mutation Average:60.836; most accessible tissue: Zhenshan97 young leaf, score: 80.589 N N N N
vg0605572207 T -> C LOC_Os06g10670-LOC_Os06g10680 intergenic_region ; MODIFIER silent_mutation Average:60.836; most accessible tissue: Zhenshan97 young leaf, score: 80.589 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0605572207 5.47E-06 4.54E-07 mr1305_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
vg0605572207 NA 2.25E-06 mr1409_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
vg0605572207 6.57E-06 2.90E-07 mr1585_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
vg0605572207 4.33E-06 4.33E-06 mr1645_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
vg0605572207 2.26E-06 2.26E-06 mr1647_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
vg0605572207 NA 8.79E-06 mr1703_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