| Variant ID: vg0100946410 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 946410 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
AATTCACAATTAATTCGGCTTCAAAATTACTTGAAACGTGCCCCCCAGCATTCTGCCTAGAACCGGTCAGACCGGCCACACAGGGCCGGTCAGACCGCTC[A/G]
GGGATGCCGGTCAGACCGGCGGCATGTGGCCGGTCAGACCGCCCCTGGTCACGGTCAGACCGGCCGTGCAACGTCGGTCAGACCGCCTCTGGTCCCCAAC
GTTGGGGACCAGAGGCGGTCTGACCGACGTTGCACGGCCGGTCTGACCGTGACCAGGGGCGGTCTGACCGGCCACATGCCGCCGGTCTGACCGGCATCCC[T/C]
GAGCGGTCTGACCGGCCCTGTGTGGCCGGTCTGACCGGTTCTAGGCAGAATGCTGGGGGGCACGTTTCAAGTAATTTTGAAGCCGAATTAATTGTGAATT
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 62.20% | 0.80% | 16.34% | 20.67% | NA |
| All Indica | 2759 | 52.60% | 0.90% | 24.28% | 22.15% | NA |
| All Japonica | 1512 | 72.30% | 0.50% | 5.09% | 22.16% | NA |
| Aus | 269 | 91.80% | 1.50% | 2.23% | 4.46% | NA |
| Indica I | 595 | 39.80% | 0.70% | 16.30% | 43.19% | NA |
| Indica II | 465 | 38.50% | 1.10% | 30.32% | 30.11% | NA |
| Indica III | 913 | 65.10% | 1.00% | 30.12% | 3.83% | NA |
| Indica Intermediate | 786 | 56.20% | 1.00% | 19.97% | 22.77% | NA |
| Temperate Japonica | 767 | 95.60% | 0.00% | 0.65% | 3.78% | NA |
| Tropical Japonica | 504 | 28.40% | 1.20% | 13.69% | 56.75% | NA |
| Japonica Intermediate | 241 | 90.00% | 0.40% | 1.24% | 8.30% | NA |
| VI/Aromatic | 96 | 91.70% | 0.00% | 7.29% | 1.04% | NA |
| Intermediate | 90 | 66.70% | 0.00% | 13.33% | 20.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0100946410 | A -> G | LOC_Os01g02740.1 | intron_variant ; MODIFIER | silent_mutation | Average:13.244; most accessible tissue: Callus, score: 27.878 | N | N | N | N |
| vg0100946410 | A -> DEL | N | N | silent_mutation | Average:13.244; most accessible tissue: Callus, score: 27.878 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0100946410 | 1.17E-06 | 8.26E-09 | mr1377 | 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 |
| vg0100946410 | 8.28E-06 | 8.28E-06 | mr1377 | 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 |