| Variant ID: vg0904682424 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 4682424 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CCCCCAATCGCTCAACGCCGATCTCCTCGTCATCAGACCGTTCAGGGGAGTGGAGGACCAAAAATCAGGTCAGACTCCCAATCCCAAACTCCCAATCTGA[C/T]
TGGGCAGACAAATTCTCGCAAGAGAAAGCTTATGCTGAACGACGACGAAGGCGACGACAATAATAAATTTGGGGATAAGGGATCACCCAAAAAATTACCA
TGGTAATTTTTTGGGTGATCCCTTATCCCCAAATTTATTATTGTCGTCGCCTTCGTCGTCGTTCAGCATAAGCTTTCTCTTGCGAGAATTTGTCTGCCCA[G/A]
TCAGATTGGGAGTTTGGGATTGGGAGTCTGACCTGATTTTTGGTCCTCCACTCCCCTGAACGGTCTGATGACGAGGAGATCGGCGTTGAGCGATTGGGGG
| 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 | 70.40% | 5.10% | 7.28% | 17.16% | NA |
| All Indica | 2759 | 63.80% | 8.30% | 8.88% | 19.03% | NA |
| All Japonica | 1512 | 76.40% | 0.10% | 5.49% | 17.99% | NA |
| Aus | 269 | 96.30% | 2.20% | 0.37% | 1.12% | NA |
| Indica I | 595 | 63.90% | 11.90% | 12.27% | 11.93% | NA |
| Indica II | 465 | 69.20% | 2.60% | 7.31% | 20.86% | NA |
| Indica III | 913 | 59.00% | 8.40% | 7.45% | 25.08% | NA |
| Indica Intermediate | 786 | 65.90% | 8.90% | 8.91% | 16.28% | NA |
| Temperate Japonica | 767 | 98.40% | 0.10% | 0.13% | 1.30% | NA |
| Tropical Japonica | 504 | 43.70% | 0.20% | 14.88% | 41.27% | NA |
| Japonica Intermediate | 241 | 74.70% | 0.00% | 2.90% | 22.41% | NA |
| VI/Aromatic | 96 | 86.50% | 0.00% | 7.29% | 6.25% | NA |
| Intermediate | 90 | 80.00% | 5.60% | 8.89% | 5.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0904682424 | C -> DEL | LOC_Os09g08860.1 | N | frameshift_variant | Average:33.119; most accessible tissue: Zhenshan97 flag leaf, score: 72.012 | N | N | N | N |
| vg0904682424 | C -> T | LOC_Os09g08860.1 | missense_variant ; p.Thr337Ile; MODERATE | nonsynonymous_codon ; T337I | Average:33.119; most accessible tissue: Zhenshan97 flag leaf, score: 72.012 | unknown | unknown | TOLERATED | 0.13 |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0904682424 | 5.61E-06 | NA | mr1113 | 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 |
| vg0904682424 | 1.97E-06 | NA | mr1158 | 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 |
| vg0904682424 | 2.28E-07 | NA | mr1158 | 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 |