| Variant ID: vg0224323458 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 24323458 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
ACTGGTCTACTGCCTCCGGAGATGGAAAATCTGGATCGGTAAAAGCGGTCGAGAACTCGAGATACGGCAGAGAAATGGACGAGGGCGCCAGATGTGACAC[T/A]
GCTGTAGAATTGTGTTTTTTAAGGCCATTGTCCAAGGACCAACTGCCCAATCTGGTACTACTTGTCTTCGGCAAAACAGATTTACAGGGAGAATTCGCAA
TTGCGAATTCTCCCTGTAAATCTGTTTTGCCGAAGACAAGTAGTACCAGATTGGGCAGTTGGTCCTTGGACAATGGCCTTAAAAAACACAATTCTACAGC[A/T]
GTGTCACATCTGGCGCCCTCGTCCATTTCTCTGCCGTATCTCGAGTTCTCGACCGCTTTTACCGATCCAGATTTTCCATCTCCGGAGGCAGTAGACCAGT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 55.40% | 6.70% | 1.16% | 36.65% | NA |
| All Indica | 2759 | 59.90% | 5.30% | 1.23% | 33.60% | NA |
| All Japonica | 1512 | 47.20% | 8.60% | 0.99% | 43.25% | NA |
| Aus | 269 | 60.60% | 3.30% | 0.74% | 35.32% | NA |
| Indica I | 595 | 72.10% | 1.80% | 0.84% | 25.21% | NA |
| Indica II | 465 | 59.40% | 4.50% | 0.43% | 35.70% | NA |
| Indica III | 913 | 55.40% | 6.80% | 1.10% | 36.69% | NA |
| Indica Intermediate | 786 | 56.10% | 6.60% | 2.16% | 35.11% | NA |
| Temperate Japonica | 767 | 40.00% | 9.90% | 1.30% | 48.76% | NA |
| Tropical Japonica | 504 | 65.30% | 6.00% | 0.60% | 28.17% | NA |
| Japonica Intermediate | 241 | 32.00% | 10.00% | 0.83% | 57.26% | NA |
| VI/Aromatic | 96 | 35.40% | 30.20% | 4.17% | 30.21% | NA |
| Intermediate | 90 | 64.40% | 5.60% | 0.00% | 30.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0224323458 | T -> A | LOC_Os02g40190.1 | synonymous_variant ; p.Thr9Thr; LOW | synonymous_codon | Average:15.043; most accessible tissue: Callus, score: 90.934 | N | N | N | N |
| vg0224323458 | T -> DEL | LOC_Os02g40190.1 | N | frameshift_variant | Average:15.043; most accessible tissue: Callus, score: 90.934 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0224323458 | NA | 5.56E-06 | mr1952 | 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 |
| vg0224323458 | 2.56E-06 | NA | mr1962 | 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 |
| vg0224323458 | NA | 7.40E-06 | mr1123_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 |
| vg0224323458 | NA | 7.35E-08 | mr1567_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 |
| vg0224323458 | NA | 6.45E-06 | mr1748_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 |