| Variant ID: vg0416678412 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 16678412 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CTTGGGCTGTCTTCTCTGCAGCTTCACCGCAAGCCGCCCAACGAGTCTACGCCAGACCCACCGTCTTCAAGAGACTCTGCTATCCACGTAATTTCTTCCT[T/C]
TTGATTCCACCTGCAACAGTGCTCCACCTTCTCACCTATCATCTCAGTCATCTTGCCAAGCGAAATTGGATTTCTTCCTAGCTGTCACATCATAGACTCC
GGAGTCTATGATGTGACAGCTAGGAAGAAATCCAATTTCGCTTGGCAAGATGACTGAGATGATAGGTGAGAAGGTGGAGCACTGTTGCAGGTGGAATCAA[A/G]
AGGAAGAAATTACGTGGATAGCAGAGTCTCTTGAAGACGGTGGGTCTGGCGTAGACTCGTTGGGCGGCTTGCGGTGAAGCTGCAGAGAAGACAGCCCAAG
| 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 | 68.60% | 0.20% | 5.50% | 25.69% | NA |
| All Indica | 2759 | 53.40% | 0.30% | 8.16% | 38.24% | NA |
| All Japonica | 1512 | 89.20% | 0.10% | 1.39% | 9.33% | NA |
| Aus | 269 | 95.50% | 0.00% | 4.09% | 0.37% | NA |
| Indica I | 595 | 63.40% | 0.00% | 2.52% | 34.12% | NA |
| Indica II | 465 | 40.90% | 0.00% | 7.53% | 51.61% | NA |
| Indica III | 913 | 58.10% | 0.10% | 10.08% | 31.76% | NA |
| Indica Intermediate | 786 | 47.70% | 0.80% | 10.56% | 40.97% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 69.40% | 0.20% | 3.97% | 26.39% | NA |
| Japonica Intermediate | 241 | 96.30% | 0.00% | 0.41% | 3.32% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 76.70% | 2.20% | 3.33% | 17.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0416678412 | T -> C | LOC_Os04g28220.1 | missense_variant ; p.Lys230Glu; MODERATE | nonsynonymous_codon ; K230E | Average:36.438; most accessible tissue: Minghui63 young leaf, score: 63.571 | unknown | unknown | TOLERATED | 1.00 |
| vg0416678412 | T -> DEL | LOC_Os04g28220.1 | N | frameshift_variant | Average:36.438; most accessible tissue: Minghui63 young leaf, score: 63.571 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0416678412 | NA | 3.19E-06 | mr1304 | 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 |
| vg0416678412 | 4.31E-06 | 3.74E-08 | 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 |
| vg0416678412 | NA | 1.11E-07 | mr1125_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 |