| Variant ID: vg1123325178 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 23325178 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TTAATTCTGAATAAAAATCATTGATCTCAACATCGGATAAGTTCTCATGAGTAAATATTTCCACAAAAATCTTGCAATGCAACCAAAGATCTACTTCATC[T/C]
AAGGATTTTAAATTTTCAGAGTTGAACAAAAACCCAAAAACATTATCAAATGCTTTCATCTGCTCAAATATATTAGTCAGTGAAGCAATTGCAGCATCAA
TTGATGCTGCAATTGCTTCACTGACTAATATATTTGAGCAGATGAAAGCATTTGATAATGTTTTTGGGTTTTTGTTCAACTCTGAAAATTTAAAATCCTT[A/G]
GATGAAGTAGATCTTTGGTTGCATTGCAAGATTTTTGTGGAAATATTTACTCATGAGAACTTATCCGATGTTGAGATCAATGATTTTTATTCAGAATTAA
| 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 | 42.80% | 9.40% | 2.31% | 45.51% | NA |
| All Indica | 2759 | 46.40% | 1.00% | 3.12% | 49.51% | NA |
| All Japonica | 1512 | 34.40% | 26.60% | 0.79% | 38.23% | NA |
| Aus | 269 | 54.30% | 1.50% | 2.23% | 42.01% | NA |
| Indica I | 595 | 59.20% | 2.40% | 1.68% | 36.81% | NA |
| Indica II | 465 | 62.40% | 1.30% | 2.80% | 33.55% | NA |
| Indica III | 913 | 25.30% | 0.10% | 2.74% | 71.85% | NA |
| Indica Intermediate | 786 | 51.70% | 0.90% | 4.83% | 42.62% | NA |
| Temperate Japonica | 767 | 20.50% | 45.50% | 0.65% | 33.38% | NA |
| Tropical Japonica | 504 | 54.00% | 6.70% | 0.79% | 38.49% | NA |
| Japonica Intermediate | 241 | 37.80% | 7.90% | 1.24% | 53.11% | NA |
| VI/Aromatic | 96 | 33.30% | 3.10% | 3.12% | 60.42% | NA |
| Intermediate | 90 | 52.20% | 5.60% | 2.22% | 40.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1123325178 | T -> DEL | N | N | silent_mutation | Average:53.742; most accessible tissue: Minghui63 flag leaf, score: 80.786 | N | N | N | N |
| vg1123325178 | T -> C | LOC_Os11g39170-LOC_Os11g39190 | intergenic_region ; MODIFIER | silent_mutation | Average:53.742; most accessible tissue: Minghui63 flag leaf, score: 80.786 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1123325178 | 2.89E-08 | 1.11E-31 | mr1137 | 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 |
| vg1123325178 | NA | 2.01E-11 | mr1137 | 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 |
| vg1123325178 | NA | 3.50E-09 | mr1486 | 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 |
| vg1123325178 | NA | 1.98E-08 | mr1617 | 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 |
| vg1123325178 | NA | 1.74E-07 | mr1629 | 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 |