| Variant ID: vg1011513758 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 11513758 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TTCCCAGAAAGATGTTCAGAAGTCGACTGTATGTATGGCGGCACTCAGCCGGTTTGTCCCACGACTCGGTGAGCGGGGGATGCCCTTTTTCAAACTATTG[A/T]
AGAAGACCGACAATTTCCAGTGAGGACCCAAGGCCCCGCAAGCCTTTGAAGATTTCAAGAAACTTCTCACAACTCCACCGGTCCTAGCATCACCACATCC
GGATGTGGTGATGCTAGGACCGGTGGAGTTGTGAGAAGTTTCTTGAAATCTTCAAAGGCTTGCGGGGCCTTGGGTCCTCACTGGAAATTGTCGGTCTTCT[T/A]
CAATAGTTTGAAAAAGGGCATCCCCCGCTCACCGAGTCGTGGGACAAACCGGCTGAGTGCCGCCATACATACAGTCGACTTCTGAACATCTTTCTGGGAA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 47.50% | 0.40% | 1.61% | 50.51% | NA |
| All Indica | 2759 | 43.00% | 0.30% | 1.96% | 54.84% | NA |
| All Japonica | 1512 | 55.80% | 0.80% | 0.40% | 43.06% | NA |
| Aus | 269 | 54.60% | 0.00% | 5.20% | 40.15% | NA |
| Indica I | 595 | 56.60% | 0.00% | 1.34% | 42.02% | NA |
| Indica II | 465 | 40.90% | 0.00% | 2.37% | 56.77% | NA |
| Indica III | 913 | 35.60% | 0.20% | 2.19% | 61.99% | NA |
| Indica Intermediate | 786 | 42.40% | 0.60% | 1.91% | 55.09% | NA |
| Temperate Japonica | 767 | 88.10% | 0.10% | 0.26% | 11.47% | NA |
| Tropical Japonica | 504 | 17.10% | 1.80% | 0.40% | 80.75% | NA |
| Japonica Intermediate | 241 | 33.60% | 0.80% | 0.83% | 64.73% | NA |
| VI/Aromatic | 96 | 19.80% | 0.00% | 1.04% | 79.17% | NA |
| Intermediate | 90 | 54.40% | 1.10% | 1.11% | 43.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1011513758 | A -> T | LOC_Os10g22250.1 | stop_gained ; p.Lys138*; HIGH | stop_gained | Average:11.403; most accessible tissue: Callus, score: 30.414 | N | N | N | N |
| vg1011513758 | A -> DEL | LOC_Os10g22250.1 | N | frameshift_variant | Average:11.403; most accessible tissue: Callus, score: 30.414 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1011513758 | NA | 1.25E-06 | mr1518 | 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 |
| vg1011513758 | NA | 1.09E-06 | mr1676 | 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 |
| vg1011513758 | 1.13E-06 | 7.67E-10 | mr1676_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 |
| vg1011513758 | NA | 7.57E-08 | mr1696_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 |