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Detailed information for vg0220315567:

Variant ID: vg0220315567 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 20315567
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGTGTCCTTTACTGTATCGATGGACACCTTGGCATACCCAGCTAGCAGGTCTACGCTGTGGACCTTGTCTGTAACCGAGGGCTTGAAAGCCATGCCCCCA[G/A]
CGACTTCGGGAGCGAAAGTTGGGTGGACCCTCGCCAGTAGGACACACTGTGCTACGCCCTGCATATGTGAAAGTCTGAATTTAATATTGGAACGTGTAAA

Reverse complement sequence

TTTACACGTTCCAATATTAAATTCAGACTTTCACATATGCAGGGCGTAGCACAGTGTGTCCTACTGGCGAGGGTCCACCCAACTTTCGCTCCCGAAGTCG[C/T]
TGGGGGCATGGCTTTCAAGCCCTCGGTTACAGACAAGGTCCACAGCGTAGACCTGCTAGCTGGGTATGCCAAGGTGTCCATCGATACAGTAAAGGACACC

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 95.00% 2.30% 2.09% 0.55% NA
All Indica  2759 98.60% 0.10% 0.54% 0.69% NA
All Japonica  1512 87.40% 6.80% 5.36% 0.40% NA
Aus  269 99.60% 0.00% 0.00% 0.37% NA
Indica I  595 99.00% 0.50% 0.17% 0.34% NA
Indica II  465 99.10% 0.00% 0.43% 0.43% NA
Indica III  913 97.70% 0.00% 0.88% 1.42% NA
Indica Intermediate  786 99.10% 0.10% 0.51% 0.25% NA
Temperate Japonica  767 77.60% 13.30% 8.87% 0.26% NA
Tropical Japonica  504 99.00% 0.00% 0.60% 0.40% NA
Japonica Intermediate  241 94.60% 0.40% 4.15% 0.83% NA
VI/Aromatic  96 97.90% 0.00% 2.08% 0.00% NA
Intermediate  90 96.70% 2.20% 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
vg0220315567 G -> A LOC_Os02g34010.1 missense_variant ; p.Ala359Val; MODERATE nonsynonymous_codon ; A359V Average:42.246; most accessible tissue: Minghui63 flag leaf, score: 76.091 benign 1.39 DELETERIOUS 0.00
vg0220315567 G -> DEL LOC_Os02g34010.1 N frameshift_variant Average:42.246; most accessible tissue: Minghui63 flag leaf, score: 76.091 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0220315567 3.49E-08 NA mr1210 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
vg0220315567 3.92E-06 4.24E-09 mr1210 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
vg0220315567 1.36E-06 NA mr1305 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
vg0220315567 NA 1.12E-07 mr1305 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
vg0220315567 2.28E-06 NA mr1585 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
vg0220315567 NA 6.88E-09 mr1585 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
vg0220315567 9.66E-09 NA mr1586 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
vg0220315567 4.68E-06 1.20E-08 mr1586 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
vg0220315567 3.81E-06 NA mr1765 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
vg0220315567 NA 3.34E-07 mr1765 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
vg0220315567 1.22E-07 NA mr1305_2 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
vg0220315567 1.20E-06 1.82E-08 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
vg0220315567 1.39E-08 2.91E-09 mr1585_2 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
vg0220315567 1.19E-06 6.95E-09 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
vg0220315567 8.34E-08 NA mr1672_2 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
vg0220315567 NA 8.30E-06 mr1672_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