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Detailed information for vg0709987989:

Variant ID: vg0709987989 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 9987989
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACCTGGTGACAAAACAGAAATGGGACACGTTTTTCATCATTTTCTGATGAGAATTTTTTTTTTCGCTGACAAAATAATGACAAATTCAAGATCACTCGCA[A/G]
AAAACATAAAAAAAATTGCTGGTTTGTTTCACATCATTATTTGTGAATTTGTGATTGTTAATCAGATCACAAAGCGATTCACGATCAGATCTGTCGTTTC

Reverse complement sequence

GAAACGACAGATCTGATCGTGAATCGCTTTGTGATCTGATTAACAATCACAAATTCACAAATAATGATGTGAAACAAACCAGCAATTTTTTTTATGTTTT[T/C]
TGCGAGTGATCTTGAATTTGTCATTATTTTGTCAGCGAAAAAAAAAATTCTCATCAGAAAATGATGAAAAACGTGTCCCATTTCTGTTTTGTCACCAGGT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 85.90% 1.00% 1.38% 11.68% NA
All Indica  2759 88.90% 0.00% 0.07% 11.05% NA
All Japonica  1512 77.20% 3.20% 3.44% 16.07% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 69.10% 0.00% 0.00% 30.92% NA
Indica II  465 94.40% 0.00% 0.22% 5.38% NA
Indica III  913 99.70% 0.00% 0.00% 0.33% NA
Indica Intermediate  786 88.00% 0.00% 0.13% 11.83% NA
Temperate Japonica  767 65.80% 5.10% 6.26% 22.82% NA
Tropical Japonica  504 99.00% 0.20% 0.00% 0.79% NA
Japonica Intermediate  241 68.00% 3.70% 1.66% 26.56% NA
VI/Aromatic  96 89.60% 0.00% 9.38% 1.04% NA
Intermediate  90 94.40% 0.00% 2.22% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0709987989 A -> DEL N N silent_mutation Average:56.654; most accessible tissue: Callus, score: 79.611 N N N N
vg0709987989 A -> G LOC_Os07g16980.1 upstream_gene_variant ; 2084.0bp to feature; MODIFIER silent_mutation Average:56.654; most accessible tissue: Callus, score: 79.611 N N N N
vg0709987989 A -> G LOC_Os07g16970.1 intron_variant ; MODIFIER silent_mutation Average:56.654; most accessible tissue: Callus, score: 79.611 N N N N
vg0709987989 A -> G LOC_Os07g16970.2 intron_variant ; MODIFIER silent_mutation Average:56.654; most accessible tissue: Callus, score: 79.611 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0709987989 NA 3.01E-08 mr1624 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
vg0709987989 NA 5.81E-09 mr1624_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
vg0709987989 NA 3.41E-10 mr1733_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
vg0709987989 NA 4.55E-07 mr1736_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
vg0709987989 NA 4.69E-06 mr1736_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
vg0709987989 NA 9.47E-06 mr1739_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
vg0709987989 NA 3.85E-08 mr1741_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
vg0709987989 NA 4.00E-06 mr1751_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
vg0709987989 NA 1.28E-06 mr1757_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
vg0709987989 NA 1.20E-06 mr1887_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