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Detailed information for vg0822299189:

Variant ID: vg0822299189 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 22299189
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GAACTACTCCCGCAGGAATTCGTCCCAAACTCGGATCCCTTGTTTCCACAAATTGGGGGTATCCTCCAGCAAAGGCTCCAAAAACACATCCATGTAATTG[C/T]
CAGGTTGTCGTGGTCCCTGTACAAGGATGGTCAACAAGATATACTTTCTTTTCTGACACAGCCACGTTAGGAGGTTGTACATGGTTAGGAGTACTGGCCA

Reverse complement sequence

TGGCCAGTACTCCTAACCATGTACAACCTCCTAACGTGGCTGTGTCAGAAAAGAAAGTATATCTTGTTGACCATCCTTGTACAGGGACCACGACAACCTG[G/A]
CAATTACATGGATGTGTTTTTGGAGCCTTTGCTGGAGGATACCCCCAATTTGTGGAAACAAGGGATCCGAGTTTGGGACGAATTCCTGCGGGAGTAGTTC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.40% 5.50% 0.11% 0.00% NA
All Indica  2759 99.20% 0.80% 0.04% 0.00% NA
All Japonica  1512 92.10% 7.60% 0.26% 0.00% NA
Aus  269 56.90% 43.10% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.30% 0.70% 0.00% 0.00% NA
Indica Intermediate  786 98.10% 1.80% 0.13% 0.00% NA
Temperate Japonica  767 96.50% 3.30% 0.26% 0.00% NA
Tropical Japonica  504 90.90% 8.90% 0.20% 0.00% NA
Japonica Intermediate  241 80.90% 18.70% 0.41% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 0.00% 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
vg0822299189 C -> T LOC_Os08g35370.1 intron_variant ; MODIFIER silent_mutation Average:42.303; most accessible tissue: Minghui63 young leaf, score: 51.901 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0822299189 1.11E-07 1.32E-12 mr1151_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
vg0822299189 NA 8.50E-08 mr1252_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
vg0822299189 NA 6.71E-07 mr1263_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
vg0822299189 NA 3.37E-07 mr1702_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
vg0822299189 NA 2.09E-06 mr1729_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
vg0822299189 NA 2.57E-06 mr1740_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