Search for Variation information by Variation ID:
Detailed information for vg0517141441:
| Variant ID: vg0517141441 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 17141441 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.90, C: 0.10, others allele: 0.00, population size: 93. )
Flanking Sequence (100 bp) in Reference Genome:
ACCTCTAAAATCAGCATCTGAATATCCACTTAAGCATATAGAAGATGAAGTAGAATACAAAATTCCAAACTCAAGTGTATGATTCAAATACCTCATTATT[T/C]
GCTTGACCGCTTGACGATGTGAAGCACGAGGAGAAGCTTGAAAGCGCGCACACAAACACACAGCAAATTGTATGTCTGACCTAGAAGTAGTTAGATACAA
Reverse complement sequence
TTGTATCTAACTACTTCTAGGTCAGACATACAATTTGCTGTGTGTTTGTGTGCGCGCTTTCAAGCTTCTCCTCGTGCTTCACATCGTCAAGCGGTCAAGC[A/G]
AATAATGAGGTATTTGAATCATACACTTGAGTTTGGAATTTTGTATTCTACTTCATCTTCTATATGCTTAAGTGGATATTCAGATGCTGATTTTAGAGGT
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 41.00% | 2.30% | 14.01% | 42.68% | NA |
| All Indica | 2759 | 14.80% | 3.50% | 15.80% | 65.89% | NA |
| All Japonica | 1512 | 91.40% | 0.20% | 0.46% | 7.94% | NA |
| Aus | 269 | 2.20% | 4.10% | 76.95% | 16.73% | NA |
| Indica I | 595 | 9.90% | 3.20% | 15.80% | 71.09% | NA |
| Indica II | 465 | 6.90% | 2.40% | 25.16% | 65.59% | NA |
| Indica III | 913 | 22.00% | 4.50% | 13.03% | 60.46% | NA |
| Indica Intermediate | 786 | 14.90% | 3.20% | 13.49% | 68.45% | NA |
| Temperate Japonica | 767 | 97.10% | 0.00% | 0.52% | 2.35% | NA |
| Tropical Japonica | 504 | 81.20% | 0.60% | 0.40% | 17.86% | NA |
| Japonica Intermediate | 241 | 94.60% | 0.00% | 0.41% | 4.98% | NA |
| VI/Aromatic | 96 | 96.90% | 0.00% | 3.12% | 0.00% | NA |
| Intermediate | 90 | 51.10% | 1.10% | 10.00% | 37.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0517141441 | T -> DEL | LOC_Os05g29174.1 | N | frameshift_variant | Average:8.585; most accessible tissue: Zhenshan97 root, score: 12.891 | N | N | N | N |
| vg0517141441 | T -> C | LOC_Os05g29174.1 | missense_variant ; p.Gln116Arg; MODERATE | nonsynonymous_codon ; Q116R | Average:8.585; most accessible tissue: Zhenshan97 root, score: 12.891 | benign  |
-0.586 |
TOLERATED | 1.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0517141441 | 3.34E-06 | NA | mr1754 | 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 |