| Variant ID: vg0100966110 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 966110 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AATCACAATCTAATTAAGGCCTAGTTTCGATGGCCCATCTAGGCCTGGCCCATCAAGTCAATCACAATCCCTTTCCGGCCCAGATATATATGTTTGTGGG[C/T]
TTTGCAAAAGGAAACTTAATTAACAAGACCACTAAAATCCTGCCATTAGCAATGGTCATCTTGATAACTTGGTCATTAGCAGGCAGCAGGTTAGCAGCTA
TAGCTGCTAACCTGCTGCCTGCTAATGACCAAGTTATCAAGATGACCATTGCTAATGGCAGGATTTTAGTGGTCTTGTTAATTAAGTTTCCTTTTGCAAA[G/A]
CCCACAAACATATATATCTGGGCCGGAAAGGGATTGTGATTGACTTGATGGGCCAGGCCTAGATGGGCCATCGAAACTAGGCCTTAATTAGATTGTGATT
| 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 | 40.60% | 3.90% | 3.77% | 51.65% | NA |
| All Indica | 2759 | 28.40% | 0.00% | 3.73% | 67.81% | NA |
| All Japonica | 1512 | 55.10% | 12.00% | 2.98% | 29.96% | NA |
| Aus | 269 | 63.60% | 0.00% | 8.92% | 27.51% | NA |
| Indica I | 595 | 12.90% | 0.00% | 3.53% | 83.53% | NA |
| Indica II | 465 | 12.90% | 0.00% | 6.02% | 81.08% | NA |
| Indica III | 913 | 42.40% | 0.10% | 2.52% | 54.98% | NA |
| Indica Intermediate | 786 | 33.10% | 0.00% | 3.94% | 62.98% | NA |
| Temperate Japonica | 767 | 85.50% | 5.30% | 3.52% | 5.61% | NA |
| Tropical Japonica | 504 | 14.70% | 8.50% | 0.79% | 75.99% | NA |
| Japonica Intermediate | 241 | 42.70% | 40.20% | 5.81% | 11.20% | NA |
| VI/Aromatic | 96 | 94.80% | 0.00% | 0.00% | 5.21% | NA |
| Intermediate | 90 | 46.70% | 4.40% | 6.67% | 42.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0100966110 | C -> T | LOC_Os01g02770.1 | downstream_gene_variant ; 959.0bp to feature; MODIFIER | silent_mutation | Average:16.724; most accessible tissue: Callus, score: 97.223 | N | N | N | N |
| vg0100966110 | C -> T | LOC_Os01g02780.1 | downstream_gene_variant ; 3198.0bp to feature; MODIFIER | silent_mutation | Average:16.724; most accessible tissue: Callus, score: 97.223 | N | N | N | N |
| vg0100966110 | C -> T | LOC_Os01g02770-LOC_Os01g02780 | intergenic_region ; MODIFIER | silent_mutation | Average:16.724; most accessible tissue: Callus, score: 97.223 | N | N | N | N |
| vg0100966110 | C -> DEL | N | N | silent_mutation | Average:16.724; most accessible tissue: Callus, score: 97.223 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0100966110 | NA | 3.48E-08 | mr1064_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 |
| vg0100966110 | NA | 9.52E-06 | mr1519_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 |
| vg0100966110 | 1.39E-06 | 1.25E-06 | mr1549_2 | 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 |
| vg0100966110 | NA | 5.74E-10 | mr1745_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 |