| Variant ID: vg0216673711 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 16673711 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TCAGCCAAGCCACCGTCAAACCAAAGAGAAGTAAGTGCTACCTGTTATGACTGTGGCGAGTAAGGTCATTATGTAAGGAACTGCCCATGGAAGGTGTTCG[C/T]
CAGGTCACTTGAAAAGGACGAGAAGCAGTGCCCAGGAAGTAACCAAGCTCCAAGTCAGCCTACCGACAAGAAGGATGGTACTTTGCAGCCCAACTCTGGA
TCCAGAGTTGGGCTGCAAAGTACCATCCTTCTTGTCGGTAGGCTGACTTGGAGCTTGGTTACTTCCTGGGCACTGCTTCTCGTCCTTTTCAAGTGACCTG[G/A]
CGAACACCTTCCATGGGCAGTTCCTTACATAATGACCTTACTCGCCACAGTCATAACAGGTAGCACTTACTTCTCTTTGGTTTGACGGTGGCTTGGCTGA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 73.20% | 9.30% | 4.85% | 12.59% | NA |
| All Indica | 2759 | 73.10% | 12.80% | 5.94% | 8.12% | NA |
| All Japonica | 1512 | 75.60% | 1.40% | 1.52% | 21.49% | NA |
| Aus | 269 | 51.30% | 21.90% | 12.64% | 14.13% | NA |
| Indica I | 595 | 68.10% | 15.30% | 9.58% | 7.06% | NA |
| Indica II | 465 | 87.50% | 6.20% | 2.80% | 3.44% | NA |
| Indica III | 913 | 67.40% | 16.20% | 5.04% | 11.39% | NA |
| Indica Intermediate | 786 | 75.20% | 10.80% | 6.11% | 7.89% | NA |
| Temperate Japonica | 767 | 96.50% | 0.00% | 0.00% | 3.52% | NA |
| Tropical Japonica | 504 | 40.90% | 4.00% | 4.37% | 50.79% | NA |
| Japonica Intermediate | 241 | 81.70% | 0.40% | 0.41% | 17.43% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 73.30% | 8.90% | 8.89% | 8.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0216673711 | C -> T | LOC_Os02g28160.1 | missense_variant ; p.Ala71Val; MODERATE | nonsynonymous_codon ; A71V | Average:42.985; most accessible tissue: Minghui63 flag leaf, score: 73.752 | unknown | unknown | DELETERIOUS | 0.01 |
| vg0216673711 | C -> DEL | LOC_Os02g28160.1 | N | frameshift_variant | Average:42.985; most accessible tissue: Minghui63 flag leaf, score: 73.752 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0216673711 | NA | 9.17E-07 | mr1586 | 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 |
| vg0216673711 | NA | 4.50E-06 | mr1305_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 |
| vg0216673711 | 7.19E-06 | 2.30E-07 | mr1409_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 |
| vg0216673711 | 1.69E-06 | 1.37E-07 | mr1559_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 |