| Variant ID: vg0808663281 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr08 | Position: 8663281 |
| Reference Allele: TTATAAACTTTAGGTC | Alternative Allele: T,CTATAAACTTTAGGTC |
| Primary Allele: TTATAAACTTTAGGTC | Secondary Allele: CTATAAACTTTAGGTC |
Inferred Ancestral Allele: Not determined.
ACTTTTAGTTGTATAGAAATACTATATATAGAAAATATTTGAATTTAAATTTGAATTTGAATTCAAATTCAAATTTGAATCGGGTATATAAACTTTTGAC[TTATAAACTTTAGGTC/T,CTATAAACTTTAGGTC]
TATAAACTTTAGGTCTATAAACTTTAGATGTATAGAAATAATATATATAAAAAAAATATTTGAATTCAAATTCAAATTTGAATCGGATATATAAACTTTT
AAAAGTTTATATATCCGATTCAAATTTGAATTTGAATTCAAATATTTTTTTTATATATATTATTTCTATACATCTAAAGTTTATAGACCTAAAGTTTATA[GACCTAAAGTTTATAA/A,GACCTAAAGTTTATAG]
GTCAAAAGTTTATATACCCGATTCAAATTTGAATTTGAATTCAAATTCAAATTTAAATTCAAATATTTTCTATATATAGTATTTCTATACAACTAAAAGT
| Populations | Population Size | Frequency of TTATAAACTTTAGGTC(primary allele) | Frequency of CTATAAACTTTAGGTC(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 92.40% | 1.30% | 3.96% | 2.07% | T: 0.30% |
| All Indica | 2759 | 95.90% | 0.00% | 2.21% | 1.78% | T: 0.04% |
| All Japonica | 1512 | 86.60% | 3.60% | 6.61% | 2.98% | T: 0.20% |
| Aus | 269 | 98.90% | 0.40% | 0.37% | 0.00% | T: 0.37% |
| Indica I | 595 | 96.60% | 0.00% | 1.34% | 1.85% | T: 0.17% |
| Indica II | 465 | 88.40% | 0.00% | 7.96% | 3.66% | NA |
| Indica III | 913 | 99.20% | 0.00% | 0.44% | 0.33% | NA |
| Indica Intermediate | 786 | 96.10% | 0.10% | 1.53% | 2.29% | NA |
| Temperate Japonica | 767 | 90.00% | 0.70% | 4.04% | 5.35% | NA |
| Tropical Japonica | 504 | 78.80% | 7.70% | 12.90% | 0.40% | T: 0.20% |
| Japonica Intermediate | 241 | 92.50% | 4.10% | 1.66% | 0.83% | T: 0.83% |
| VI/Aromatic | 96 | 67.70% | 1.00% | 21.88% | 1.04% | T: 8.33% |
| Intermediate | 90 | 87.80% | 3.30% | 4.44% | 3.33% | T: 1.11% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0808663281 | TTATAAACTTTAGGTC -> T | LOC_Os08g14430-LOC_Os08g14440 | intergenic_region ; MODIFIER | silent_mutation | Average:22.651; most accessible tissue: Minghui63 panicle, score: 34.226 | N | N | N | N |
| vg0808663281 | TTATAAACTTTAGGTC -> CTATAAACTTTAGGTC | LOC_Os08g14430-LOC_Os08g14440 | intergenic_region ; MODIFIER | silent_mutation | Average:22.651; most accessible tissue: Minghui63 panicle, score: 34.226 | N | N | N | N |
| vg0808663281 | TTATAAACTTTAGGTC -> DEL | N | N | silent_mutation | Average:22.651; most accessible tissue: Minghui63 panicle, score: 34.226 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0808663281 | NA | 9.24E-06 | mr1116 | 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 |
| vg0808663281 | 4.16E-06 | 6.88E-07 | mr1117 | 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 |
| vg0808663281 | 4.55E-06 | NA | mr1448 | 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 |
| vg0808663281 | 7.64E-06 | 3.68E-06 | mr1117_2 | 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 |