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Detailed information for vg0505835317:

Variant ID: vg0505835317 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 5835317
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTTTGAAGACCTCAAATTTGTATATTACCACTAAAAATATTTGCTTAAAATTTTGACAGCACCTCCCTCCCTCAAAGCTTAATTTTGAAGCAATGGCTCG[G/A]
GCTGGAGGAGAAAGAATGGGTATATAAAGCTGTGCAACTTTAGTCCCGGTTGGTAACACCAACCGGGCATAAAGATCTCAAATCACTTTAGTCCCGGTTT

Reverse complement sequence

AAACCGGGACTAAAGTGATTTGAGATCTTTATGCCCGGTTGGTGTTACCAACCGGGACTAAAGTTGCACAGCTTTATATACCCATTCTTTCTCCTCCAGC[C/T]
CGAGCCATTGCTTCAAAATTAAGCTTTGAGGGAGGGAGGTGCTGTCAAAATTTTAAGCAAATATTTTTAGTGGTAATATACAAATTTGAGGTCTTCAAAA

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 78.00% 21.80% 0.21% 0.00% NA
All Indica  2759 95.00% 4.70% 0.22% 0.00% NA
All Japonica  1512 59.30% 40.70% 0.00% 0.00% NA
Aus  269 8.60% 91.10% 0.37% 0.00% NA
Indica I  595 99.00% 1.00% 0.00% 0.00% NA
Indica II  465 94.20% 5.80% 0.00% 0.00% NA
Indica III  913 96.90% 2.60% 0.44% 0.00% NA
Indica Intermediate  786 90.30% 9.40% 0.25% 0.00% NA
Temperate Japonica  767 94.30% 5.70% 0.00% 0.00% NA
Tropical Japonica  504 11.50% 88.50% 0.00% 0.00% NA
Japonica Intermediate  241 48.10% 51.90% 0.00% 0.00% NA
VI/Aromatic  96 83.30% 14.60% 2.08% 0.00% NA
Intermediate  90 72.20% 26.70% 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
vg0505835317 G -> A LOC_Os05g10660.1 upstream_gene_variant ; 486.0bp to feature; MODIFIER silent_mutation Average:34.319; most accessible tissue: Minghui63 young leaf, score: 49.581 N N N N
vg0505835317 G -> A LOC_Os05g10660-LOC_Os05g10670 intergenic_region ; MODIFIER silent_mutation Average:34.319; most accessible tissue: Minghui63 young leaf, score: 49.581 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0505835317 NA 2.23E-14 Grain_thickness Jap_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
vg0505835317 NA 8.76E-06 mr1124 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
vg0505835317 NA 1.35E-16 mr1593 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
vg0505835317 NA 1.36E-08 mr1125_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
vg0505835317 NA 1.88E-07 mr1250_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
vg0505835317 NA 2.60E-08 mr1304_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
vg0505835317 NA 4.34E-08 mr1363_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
vg0505835317 NA 9.82E-09 mr1363_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
vg0505835317 NA 8.02E-08 mr1696_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
vg0505835317 NA 6.46E-07 mr1819_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