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Detailed information for vg0419784082:

Variant ID: vg0419784082 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 19784082
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGGCTTAATAAATTCGTCTCGCGGTTTACTGACGGATTCTGTAATTAGTTTTTTTATTAGTATCCGAACACCCTATGCGACACTCTATATATATATACCA[C/T]
ATGTAACACGCCAAAACTTTACACCCTTGGATCTAAACACCCCAGCACCCCATGGCAGCACAGTTATCATCTGACTGATCATTATCTGCAGGTTGACCAT

Reverse complement sequence

ATGGTCAACCTGCAGATAATGATCAGTCAGATGATAACTGTGCTGCCATGGGGTGCTGGGGTGTTTAGATCCAAGGGTGTAAAGTTTTGGCGTGTTACAT[G/A]
TGGTATATATATATAGAGTGTCGCATAGGGTGTTCGGATACTAATAAAAAAACTAATTACAGAATCCGTCAGTAAACCGCGAGACGAATTTATTAAGCCT

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 63.10% 36.40% 0.49% 0.00% NA
All Indica  2759 94.10% 5.70% 0.22% 0.00% NA
All Japonica  1512 14.90% 84.30% 0.73% 0.00% NA
Aus  269 40.50% 58.40% 1.12% 0.00% NA
Indica I  595 93.30% 6.40% 0.34% 0.00% NA
Indica II  465 94.40% 4.70% 0.86% 0.00% NA
Indica III  913 95.70% 4.30% 0.00% 0.00% NA
Indica Intermediate  786 92.70% 7.30% 0.00% 0.00% NA
Temperate Japonica  767 22.20% 76.80% 1.04% 0.00% NA
Tropical Japonica  504 2.20% 97.60% 0.20% 0.00% NA
Japonica Intermediate  241 18.70% 80.50% 0.83% 0.00% NA
VI/Aromatic  96 22.90% 77.10% 0.00% 0.00% NA
Intermediate  90 30.00% 66.70% 3.33% 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
vg0419784082 C -> T LOC_Os04g32780-LOC_Os04g32790 intergenic_region ; MODIFIER silent_mutation Average:56.492; most accessible tissue: Minghui63 panicle, score: 79.811 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0419784082 NA 1.10E-08 mr1047 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
vg0419784082 NA 7.35E-10 mr1151 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
vg0419784082 NA 5.08E-18 mr1164 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
vg0419784082 NA 3.09E-08 mr1174 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
vg0419784082 NA 1.12E-14 mr1261 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
vg0419784082 NA 7.75E-06 mr1450 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
vg0419784082 NA 1.91E-20 mr1580 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
vg0419784082 NA 2.53E-20 mr1627 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
vg0419784082 NA 1.80E-06 mr1627 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
vg0419784082 NA 6.10E-20 mr1825 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
vg0419784082 NA 9.38E-07 mr1321_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
vg0419784082 NA 1.55E-12 mr1514_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