| Variant ID: vg1004721424 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 4721424 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CTGGCCTACCCAGAACGTCATCAGGCCACGACTCTATTTGGGTAATAGTCGACAGACTTACCAAAGTGGCTCATTTCATCCCAGTAAAGACAACATATTC[C/T]
GGAAGCTGGTTGGCGGAATTGTATACGGCAAGGATTGTGTGTTTGCATGGCGTCCCTAAGAAAATAGTGTCTGATCGAGGTAGTTAGTTTACTTCAAAGT
ACTTTGAAGTAAACTAACTACCTCGATCAGACACTATTTTCTTAGGGACGCCATGCAAACACACAATCCTTGCCGTATACAATTCCGCCAACCAGCTTCC[G/A]
GAATATGTTGTCTTTACTGGGATGAAATGAGCCACTTTGGTAAGTCTGTCGACTATTACCCAAATAGAGTCGTGGCCTGATGACGTTCTGGGTAGGCCAG
| 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 | 75.40% | 6.30% | 5.71% | 12.53% | NA |
| All Indica | 2759 | 82.60% | 0.70% | 7.83% | 8.88% | NA |
| All Japonica | 1512 | 76.30% | 16.40% | 0.60% | 6.68% | NA |
| Aus | 269 | 6.70% | 0.00% | 7.43% | 85.87% | NA |
| Indica I | 595 | 60.70% | 0.00% | 16.30% | 23.03% | NA |
| Indica II | 465 | 89.50% | 0.00% | 4.09% | 6.45% | NA |
| Indica III | 913 | 91.90% | 0.80% | 4.93% | 2.41% | NA |
| Indica Intermediate | 786 | 84.40% | 1.50% | 7.00% | 7.12% | NA |
| Temperate Japonica | 767 | 94.40% | 0.40% | 0.39% | 4.82% | NA |
| Tropical Japonica | 504 | 54.80% | 41.90% | 0.99% | 2.38% | NA |
| Japonica Intermediate | 241 | 63.90% | 14.10% | 0.41% | 21.58% | NA |
| VI/Aromatic | 96 | 52.10% | 22.90% | 17.71% | 7.29% | NA |
| Intermediate | 90 | 71.10% | 11.10% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1004721424 | C -> T | LOC_Os10g08702.1 | synonymous_variant ; p.Ser1065Ser; LOW | synonymous_codon | Average:13.938; most accessible tissue: Callus, score: 20.8 | N | N | N | N |
| vg1004721424 | C -> DEL | LOC_Os10g08702.1 | N | frameshift_variant | Average:13.938; most accessible tissue: Callus, score: 20.8 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1004721424 | NA | 6.33E-06 | mr1188 | 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 |
| vg1004721424 | NA | 4.39E-09 | mr1570 | 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 |
| vg1004721424 | NA | 1.97E-06 | mr1077_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 |
| vg1004721424 | NA | 7.58E-09 | mr1188_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 |
| vg1004721424 | 4.95E-07 | NA | mr1961_2 | 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 |