| Variant ID: vg0402260566 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 2260566 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
TTGCCACACGCATCAGCTTCAATAGTGAACTCCATAGAAAAGTCTGGCAAAGATAAAACTGGGCTGGTGCACATTTTCTATTTTAACTTATCAAAAGCTT[A/C]
TGTCTGTAAATTTCCCCACTGAAACAATTCTTTCTTCAGCATATCATGCAATGGCCTGCATATTAATCCATAGTTCTGAATGAATCTTCTATAATACCCA
TGGGTATTATAGAAGATTCATTCAGAACTATGGATTAATATGCAGGCCATTGCATGATATGCTGAAGAAAGAATTGTTTCAGTGGGGAAATTTACAGACA[T/G]
AAGCTTTTGATAAGTTAAAATAGAAAATGTGCACCAGCCCAGTTTTATCTTTGCCAGACTTTTCTATGGAGTTCACTATTGAAGCTGATGCGTGTGGCAA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 26.50% | 16.50% | 1.04% | 55.90% | NA |
| All Indica | 2759 | 13.70% | 11.80% | 0.83% | 73.65% | NA |
| All Japonica | 1512 | 54.70% | 14.20% | 0.33% | 30.82% | NA |
| Aus | 269 | 3.70% | 77.30% | 1.49% | 17.47% | NA |
| Indica I | 595 | 5.70% | 0.50% | 1.18% | 92.61% | NA |
| Indica II | 465 | 3.70% | 1.70% | 0.65% | 93.98% | NA |
| Indica III | 913 | 20.80% | 26.60% | 0.66% | 51.92% | NA |
| Indica Intermediate | 786 | 17.60% | 9.00% | 0.89% | 72.52% | NA |
| Temperate Japonica | 767 | 87.70% | 3.90% | 0.13% | 8.21% | NA |
| Tropical Japonica | 504 | 18.50% | 18.50% | 0.79% | 62.30% | NA |
| Japonica Intermediate | 241 | 25.30% | 37.80% | 0.00% | 36.93% | NA |
| VI/Aromatic | 96 | 9.40% | 18.80% | 16.67% | 55.21% | NA |
| Intermediate | 90 | 31.10% | 18.90% | 1.11% | 48.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0402260566 | A -> C | LOC_Os04g04710.1 | stop_lost&splice_region_variant ; p.Ter731Gluext*?; HIGH | stop_lost | Average:10.268; most accessible tissue: Callus, score: 59.055 | N | N | N | N |
| vg0402260566 | A -> DEL | LOC_Os04g04710.1 | N | frameshift_variant | Average:10.268; most accessible tissue: Callus, score: 59.055 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0402260566 | NA | 1.98E-07 | mr1798 | 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 |
| vg0402260566 | NA | 4.93E-06 | mr1404_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 |
| vg0402260566 | 1.08E-06 | 5.66E-10 | mr1798_2 | Ind_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 |