| Variant ID: vg0139714293 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 39714293 |
| Reference Allele: G | Alternative Allele: C |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
TTTGGTGGTAGCCAGAGTAAGCGTCGATGAAGCTCAATAACTCGCAACCGGCTGTTGAATCCACCAGTTGGTCTATTCGAGGAAGTGGAAAGTGATCCTT[G/C]
GGGCACGCCTTGTTGAGGTCGGTGAAGTCGACACTCATTCTCCATTTTCCGTTGGCCTTCCGCACCATGACTGGATTGGCTAGCCACTCTGGATGAAGTA
TACTTCATCCAGAGTGGCTAGCCAATCCAGTCATGGTGCGGAAGGCCAACGGAAAATGGAGAATGAGTGTCGACTTCACCGACCTCAACAAGGCGTGCCC[C/G]
AAGGATCACTTTCCACTTCCTCGAATAGACCAACTGGTGGATTCAACAGCCGGTTGCGAGTTATTGAGCTTCATCGACGCTTACTCTGGCTACCACCAAA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 94.80% | 2.60% | 2.03% | 0.61% | NA |
| All Indica | 2759 | 93.80% | 3.50% | 2.68% | 0.00% | NA |
| All Japonica | 1512 | 97.70% | 0.20% | 0.20% | 1.92% | NA |
| Aus | 269 | 86.60% | 7.40% | 5.95% | 0.00% | NA |
| Indica I | 595 | 88.60% | 6.70% | 4.71% | 0.00% | NA |
| Indica II | 465 | 90.10% | 5.60% | 4.30% | 0.00% | NA |
| Indica III | 913 | 98.50% | 0.90% | 0.66% | 0.00% | NA |
| Indica Intermediate | 786 | 94.70% | 2.80% | 2.54% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 93.80% | 0.00% | 0.60% | 5.56% | NA |
| Japonica Intermediate | 241 | 98.30% | 1.20% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 94.40% | 3.30% | 2.22% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0139714293 | G -> DEL | LOC_Os01g68350.1 | N | frameshift_variant | Average:15.33; most accessible tissue: Callus, score: 25.42 | N | N | N | N |
| vg0139714293 | G -> C | LOC_Os01g68350.1 | synonymous_variant ; p.Pro792Pro; LOW | synonymous_codon | Average:15.33; most accessible tissue: Callus, score: 25.42 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0139714293 | 1.16E-06 | NA | mr1542 | 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 |
| vg0139714293 | NA | 4.96E-09 | mr1542 | 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 |
| vg0139714293 | NA | 6.04E-09 | mr1542_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 |
| vg0139714293 | NA | 3.75E-06 | mr1587_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 |