Search for Variation information by Variation ID:
Detailed information for vg0402684408:
| Variant ID: vg0402684408 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 2684408 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CGTCAAAACGGGACCAATGACTTTGTCCTCGGAGGCAATATATAACCGAAAAGGCTTTCCGGCTTTAGGCGCTCGCACAACAGGTGGAGTAGATAAATAC[T/C]
TCTTCAACTCTTCAAACGCCTCTTGTTGTTTTGCCCCCCAAGTGAAATCGGCTTCTTTTTTCAAACGAAGTATAGAAAAAAAAGCATCGATTTTACCCGC
Reverse complement sequence
GCGGGTAAAATCGATGCTTTTTTTTCTATACTTCGTTTGAAAAAAGAAGCCGATTTCACTTGGGGGGCAAAACAACAAGAGGCGTTTGAAGAGTTGAAGA[A/G]
GTATTTATCTACTCCACCTGTTGTGCGAGCGCCTAAAGCCGGAAAGCCTTTTCGGTTATATATTGCCTCCGAGGACAAAGTCATTGGTCCCGTTTTGACG
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 | 66.90% | 11.00% | 12.25% | 9.75% | NA |
| All Indica | 2759 | 66.20% | 17.70% | 15.62% | 0.51% | NA |
| All Japonica | 1512 | 62.30% | 0.50% | 7.74% | 29.43% | NA |
| Aus | 269 | 88.50% | 6.70% | 4.83% | 0.00% | NA |
| Indica I | 595 | 95.10% | 2.20% | 2.02% | 0.67% | NA |
| Indica II | 465 | 71.40% | 14.00% | 14.41% | 0.22% | NA |
| Indica III | 913 | 45.90% | 31.10% | 22.89% | 0.11% | NA |
| Indica Intermediate | 786 | 64.90% | 15.90% | 18.19% | 1.02% | NA |
| Temperate Japonica | 767 | 88.00% | 0.10% | 2.35% | 9.52% | NA |
| Tropical Japonica | 504 | 35.70% | 0.40% | 13.49% | 50.40% | NA |
| Japonica Intermediate | 241 | 36.10% | 2.10% | 12.86% | 48.96% | NA |
| VI/Aromatic | 96 | 94.80% | 1.00% | 3.12% | 1.04% | NA |
| Intermediate | 90 | 73.30% | 8.90% | 16.67% | 1.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0402684408 | T -> C | LOC_Os04g05370.1 | missense_variant ; p.Lys969Arg; MODERATE | nonsynonymous_codon ; K969R | Average:15.127; most accessible tissue: Zhenshan97 flag leaf, score: 27.583 | benign  |
-0.109 |
TOLERATED | 0.85 |
| vg0402684408 | T -> DEL | LOC_Os04g05370.1 | N | frameshift_variant | Average:15.127; most accessible tissue: Zhenshan97 flag leaf, score: 27.583 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0402684408 | NA | 5.93E-06 | mr1080 | Ind_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 |
| vg0402684408 | 3.67E-06 | NA | mr1702 | Jap_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 |
| vg0402684408 | NA | 6.00E-07 | mr1619_2 | Ind_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 |