| Variant ID: vg0821073577 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 21073577 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GTGACCTGTAGAATTTTTTTTCTCTCCTCTCTCTCCGAACTAGTGTAGAGGAGAGAGATGTGCAACTTTTTTATTTTTATTTTATTGATATTTTTTTTCA[T/C]
ACTTAGGAACTCACAAGAACCAACCATATAAAAAATAAACTCAAACGGACGAAATATGTGGCCTGTGGAATTTTTCAAAGCTCTACCGAAAAACTTCTCT
AGAGAAGTTTTTCGGTAGAGCTTTGAAAAATTCCACAGGCCACATATTTCGTCCGTTTGAGTTTATTTTTTATATGGTTGGTTCTTGTGAGTTCCTAAGT[A/G]
TGAAAAAAAATATCAATAAAATAAAAATAAAAAAGTTGCACATCTCTCTCCTCTACACTAGTTCGGAGAGAGAGGAGAGAAAAAAAATTCTACAGGTCAC
| 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 | 68.90% | 28.10% | 1.88% | 1.12% | NA |
| All Indica | 2759 | 93.90% | 1.30% | 2.86% | 1.85% | NA |
| All Japonica | 1512 | 22.40% | 77.10% | 0.46% | 0.00% | NA |
| Aus | 269 | 98.50% | 1.50% | 0.00% | 0.00% | NA |
| Indica I | 595 | 93.90% | 0.80% | 3.70% | 1.51% | NA |
| Indica II | 465 | 92.70% | 1.30% | 2.58% | 3.44% | NA |
| Indica III | 913 | 95.50% | 1.50% | 2.08% | 0.88% | NA |
| Indica Intermediate | 786 | 92.90% | 1.50% | 3.31% | 2.29% | NA |
| Temperate Japonica | 767 | 3.40% | 96.20% | 0.39% | 0.00% | NA |
| Tropical Japonica | 504 | 48.20% | 51.40% | 0.40% | 0.00% | NA |
| Japonica Intermediate | 241 | 29.00% | 70.10% | 0.83% | 0.00% | NA |
| VI/Aromatic | 96 | 12.50% | 87.50% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 52.20% | 42.20% | 3.33% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0821073577 | T -> C | LOC_Os08g33740.1 | upstream_gene_variant ; 4562.0bp to feature; MODIFIER | silent_mutation | Average:31.899; most accessible tissue: Minghui63 panicle, score: 59.629 | N | N | N | N |
| vg0821073577 | T -> C | LOC_Os08g33730-LOC_Os08g33740 | intergenic_region ; MODIFIER | silent_mutation | Average:31.899; most accessible tissue: Minghui63 panicle, score: 59.629 | N | N | N | N |
| vg0821073577 | T -> DEL | N | N | silent_mutation | Average:31.899; most accessible tissue: Minghui63 panicle, score: 59.629 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0821073577 | NA | 5.18E-15 | mr1410 | 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 |
| vg0821073577 | 3.37E-06 | NA | mr1504 | 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 |
| vg0821073577 | NA | 5.67E-06 | mr1681 | 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 |
| vg0821073577 | NA | 1.18E-13 | mr1410_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 |
| vg0821073577 | NA | 3.66E-08 | mr1746_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 |