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Detailed information for vg0706194043:

Variant ID: vg0706194043 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 6194043
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCCTCGGCTGCTTGGGACATACCCTCCTCTTCCACTCTGCCGCCTCCTGCTCCTGAGCGCCCTGCCTCTGTGGCTCGTCGTGAGCCGTCTCCCTTATTCC[A/G]
CAATTTACGGAGTCTTTTTGGTCTTTGCTCCACGGAGGCCAAAAAGAACCGCCGATTGCGGAATTCGGCGAAGAAAACGGCTCGTGATGTCAAGTTCCTC

Reverse complement sequence

GAGGAACTTGACATCACGAGCCGTTTTCTTCGCCGAATTCCGCAATCGGCGGTTCTTTTTGGCCTCCGTGGAGCAAAGACCAAAAAGACTCCGTAAATTG[T/C]
GGAATAAGGGAGACGGCTCACGACGAGCCACAGAGGCAGGGCGCTCAGGAGCAGGAGGCGGCAGAGTGGAAGAGGAGGGTATGTCCCAAGCAGCCGAGGA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 62.00% 15.80% 18.51% 3.72% NA
All Indica  2759 67.90% 6.40% 20.80% 4.89% NA
All Japonica  1512 57.80% 36.20% 6.02% 0.00% NA
Aus  269 9.70% 2.20% 74.72% 13.38% NA
Indica I  595 53.90% 10.40% 27.56% 8.07% NA
Indica II  465 82.80% 9.00% 7.96% 0.22% NA
Indica III  913 71.90% 3.20% 21.25% 3.72% NA
Indica Intermediate  786 65.10% 5.50% 22.77% 6.62% NA
Temperate Japonica  767 39.40% 52.20% 8.47% 0.00% NA
Tropical Japonica  504 86.90% 9.50% 3.57% 0.00% NA
Japonica Intermediate  241 55.60% 41.10% 3.32% 0.00% NA
VI/Aromatic  96 95.80% 2.10% 2.08% 0.00% NA
Intermediate  90 68.90% 17.80% 7.78% 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
vg0706194043 A -> DEL LOC_Os07g11240.1 N frameshift_variant Average:53.942; most accessible tissue: Minghui63 flag leaf, score: 77.153 N N N N
vg0706194043 A -> G LOC_Os07g11240.1 missense_variant ; p.His1640Arg; MODERATE nonsynonymous_codon ; H1640R Average:53.942; most accessible tissue: Minghui63 flag leaf, score: 77.153 unknown unknown TOLERATED 1.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0706194043 NA 2.15E-14 mr1035 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
vg0706194043 NA 3.23E-07 mr1097 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
vg0706194043 NA 4.41E-06 mr1149 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
vg0706194043 NA 2.69E-08 mr1252 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
vg0706194043 NA 3.18E-06 mr1387 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
vg0706194043 3.44E-06 6.59E-14 mr1626 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
vg0706194043 5.49E-06 NA mr1773 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
vg0706194043 4.33E-06 4.33E-06 mr1773 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
vg0706194043 2.41E-06 2.41E-06 mr1994 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