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Detailed information for vg0907776072:

Variant ID: vg0907776072 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 7776072
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTTTTATTTTTTTACTATTAATAGTCAAAGTTGAAAATGTTTGACTTGTCACTATGCTAAAAATGCTTATATTTTGGGATGAAGGGAGTATTCAATTTCA[A/C]
GCACGAAGCAGGTTTTGAAATTTCCAAACCCCCCCCCCCCAACCGGTAAGATCATATCTCACCCAAAATTTTCCATTTTATGCAATTTTTTGTGATTTTT

Reverse complement sequence

AAAAATCACAAAAAATTGCATAAAATGGAAAATTTTGGGTGAGATATGATCTTACCGGTTGGGGGGGGGGGGTTTGGAAATTTCAAAACCTGCTTCGTGC[T/G]
TGAAATTGAATACTCCCTTCATCCCAAAATATAAGCATTTTTAGCATAGTGACAAGTCAAACATTTTCAACTTTGACTATTAATAGTAAAAAAATAAAAA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 60.80% 36.40% 0.25% 2.60% NA
All Indica  2759 84.10% 15.40% 0.29% 0.22% NA
All Japonica  1512 32.10% 61.20% 0.20% 6.48% NA
Aus  269 5.60% 87.40% 0.00% 7.06% NA
Indica I  595 90.30% 9.70% 0.00% 0.00% NA
Indica II  465 89.90% 10.10% 0.00% 0.00% NA
Indica III  913 80.60% 19.20% 0.22% 0.00% NA
Indica Intermediate  786 80.20% 18.30% 0.76% 0.76% NA
Temperate Japonica  767 56.60% 33.40% 0.13% 9.91% NA
Tropical Japonica  504 2.40% 94.00% 0.20% 3.37% NA
Japonica Intermediate  241 16.60% 80.90% 0.41% 2.07% NA
VI/Aromatic  96 4.20% 95.80% 0.00% 0.00% NA
Intermediate  90 51.10% 47.80% 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
vg0907776072 A -> DEL N N silent_mutation Average:25.503; most accessible tissue: Callus, score: 35.373 N N N N
vg0907776072 A -> C LOC_Os09g13450.1 upstream_gene_variant ; 3288.0bp to feature; MODIFIER silent_mutation Average:25.503; most accessible tissue: Callus, score: 35.373 N N N N
vg0907776072 A -> C LOC_Os09g13430.1 downstream_gene_variant ; 2904.0bp to feature; MODIFIER silent_mutation Average:25.503; most accessible tissue: Callus, score: 35.373 N N N N
vg0907776072 A -> C LOC_Os09g13440.1 intron_variant ; MODIFIER silent_mutation Average:25.503; most accessible tissue: Callus, score: 35.373 N N N N
vg0907776072 A -> C LOC_Os09g13440.2 intron_variant ; MODIFIER silent_mutation Average:25.503; most accessible tissue: Callus, score: 35.373 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0907776072 NA 2.93E-21 Plant_height All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0907776072 NA 1.10E-07 mr1031 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
vg0907776072 NA 3.84E-06 mr1056 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
vg0907776072 NA 5.89E-09 mr1486 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
vg0907776072 NA 1.54E-06 mr1543 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
vg0907776072 NA 2.37E-08 mr1570 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
vg0907776072 NA 3.72E-06 mr1798 Ind_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
vg0907776072 NA 6.13E-07 mr1013_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
vg0907776072 NA 4.64E-08 mr1031_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
vg0907776072 NA 5.93E-06 mr1346_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
vg0907776072 NA 5.60E-09 mr1543_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
vg0907776072 2.26E-06 2.26E-06 mr1568_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
vg0907776072 NA 4.60E-06 mr1621_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
vg0907776072 NA 4.01E-07 mr1680_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