| Variant ID: vg1126800419 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 26800419 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GTTTTTTATATAATGCCGTGCATTCCTGGTATGCTCTTCTCTCTCTTCTGGAAATCTACATATGTCCAGTTTCAGAAACGAGGAAGGTGCCTAAGTTGGA[A/T]
TCATTCCCCGTGTTAATTTTCAGAGTTTCTTCAAGCAGAGACAGTTTTTAGACTTGTACAGTGCCTGGAAGCTATTCTGACTGGATTTTTCACATTTTAG
CTAAAATGTGAAAAATCCAGTCAGAATAGCTTCCAGGCACTGTACAAGTCTAAAAACTGTCTCTGCTTGAAGAAACTCTGAAAATTAACACGGGGAATGA[T/A]
TCCAACTTAGGCACCTTCCTCGTTTCTGAAACTGGACATATGTAGATTTCCAGAAGAGAGAGAAGAGCATACCAGGAATGCACGGCATTATATAAAAAAC
| 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 | 67.10% | 9.80% | 3.68% | 19.47% | NA |
| All Indica | 2759 | 54.80% | 13.00% | 6.09% | 26.06% | NA |
| All Japonica | 1512 | 86.40% | 4.60% | 0.20% | 8.80% | NA |
| Aus | 269 | 72.90% | 6.30% | 0.37% | 20.45% | NA |
| Indica I | 595 | 82.20% | 1.30% | 6.22% | 10.25% | NA |
| Indica II | 465 | 44.90% | 3.70% | 1.94% | 49.46% | NA |
| Indica III | 913 | 43.80% | 26.20% | 9.09% | 20.92% | NA |
| Indica Intermediate | 786 | 52.80% | 12.10% | 4.96% | 30.15% | NA |
| Temperate Japonica | 767 | 89.80% | 0.40% | 0.26% | 9.52% | NA |
| Tropical Japonica | 504 | 80.60% | 13.30% | 0.20% | 5.95% | NA |
| Japonica Intermediate | 241 | 87.60% | 0.00% | 0.00% | 12.45% | NA |
| VI/Aromatic | 96 | 90.60% | 8.30% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 74.40% | 10.00% | 2.22% | 13.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1126800419 | A -> T | LOC_Os11g44340.1 | intron_variant ; MODIFIER | silent_mutation | Average:60.437; most accessible tissue: Zhenshan97 root, score: 82.549 | N | N | N | N |
| vg1126800419 | A -> DEL | N | N | silent_mutation | Average:60.437; most accessible tissue: Zhenshan97 root, score: 82.549 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1126800419 | 2.84E-06 | NA | mr1471 | 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 |
| vg1126800419 | NA | 6.73E-06 | mr1808 | 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 |
| vg1126800419 | NA | 4.16E-10 | mr1471_2 | 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 |
| vg1126800419 | NA | 6.60E-09 | mr1642_2 | 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 |