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Detailed information for vg0819146214:

Variant ID: vg0819146214 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 19146214
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTGCTTATGATCCTATGTACAATCAGCTCATGATTGTGCATAGGTTCACTGAAGGGTTGCGTTTTGACATTCGTCATGCTGTTATGATGCAACGTCCTCG[C/A]
GACCTAGAGACTACTCTGGCTATTGCTTGTTTACAGGAGGAATGGATGGAGACTCAGAAGCCCAAGGAATTTCGTAAATTGGGTGATCATGTTCCGCGGA

Reverse complement sequence

TCCGCGGAACATGATCACCCAATTTACGAAATTCCTTGGGCTTCTGAGTCTCCATCCATTCCTCCTGTAAACAAGCAATAGCCAGAGTAGTCTCTAGGTC[G/T]
CGAGGACGTTGCATCATAACAGCATGACGAATGTCAAAACGCAACCCTTCAGTGAACCTATGCACAATCATGAGCTGATTGTACATAGGATCATAAGCAA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 95.40% 2.30% 2.26% 0.00% NA
All Indica  2759 98.20% 0.90% 0.87% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 39.00% 30.50% 30.48% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 98.30% 0.90% 0.86% 0.00% NA
Indica III  913 98.80% 0.50% 0.66% 0.00% NA
Indica Intermediate  786 96.20% 2.00% 1.78% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 1.10% 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
vg0819146214 C -> A LOC_Os08g31010.1 synonymous_variant ; p.Arg321Arg; LOW synonymous_codon Average:19.941; most accessible tissue: Zhenshan97 root, score: 30.989 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0819146214 NA 4.44E-15 mr1113 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
vg0819146214 NA 3.40E-19 mr1114 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
vg0819146214 NA 1.15E-18 mr1117 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
vg0819146214 NA 8.90E-23 mr1123 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
vg0819146214 NA 1.61E-14 mr1496 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
vg0819146214 9.50E-08 5.92E-40 mr1549 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
vg0819146214 6.85E-08 3.21E-45 mr1550 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
vg0819146214 1.64E-07 8.13E-42 mr1757 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
vg0819146214 NA 2.10E-31 mr1549_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
vg0819146214 NA 3.60E-46 mr1550_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
vg0819146214 NA 9.92E-28 mr1757_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