| Variant ID: vg1011329733 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 11329733 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
CAGGATTCATAAGGCTTCCCTTAAACCTATGCCGGCTACATGTTCCTTGAACATGTTGGGTGGTAGGCCTTTCGTGAGCGGATCCGCGAGCATCCTTTCT[A/G]
TTCTAATGTGCTCGAGACTGATTATTTGATCCCGGACTTTGTCCTTCACAACATAGTACTTTATGTCAATGTGTTTGGCAGCACCACTTGACTGATTGTT
AACAATCAGTCAAGTGGTGCTGCCAAACACATTGACATAAAGTACTATGTTGTGAAGGACAAAGTCCGGGATCAAATAATCAGTCTCGAGCACATTAGAA[T/C]
AGAAAGGATGCTCGCGGATCCGCTCACGAAAGGCCTACCACCCAACATGTTCAAGGAACATGTAGCCGGCATAGGTTTAAGGGAAGCCTTATGAATCCTG
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 15.20% | 0.20% | 1.99% | 82.61% | NA |
| All Indica | 2759 | 2.10% | 0.30% | 2.25% | 95.36% | NA |
| All Japonica | 1512 | 41.80% | 0.10% | 0.99% | 57.14% | NA |
| Aus | 269 | 2.20% | 0.00% | 2.97% | 94.80% | NA |
| Indica I | 595 | 2.90% | 0.20% | 1.51% | 95.46% | NA |
| Indica II | 465 | 3.00% | 0.60% | 0.22% | 96.13% | NA |
| Indica III | 913 | 0.90% | 0.20% | 3.07% | 95.84% | NA |
| Indica Intermediate | 786 | 2.30% | 0.40% | 3.05% | 94.27% | NA |
| Temperate Japonica | 767 | 68.60% | 0.00% | 0.65% | 30.77% | NA |
| Tropical Japonica | 504 | 15.90% | 0.00% | 1.59% | 82.54% | NA |
| Japonica Intermediate | 241 | 10.80% | 0.40% | 0.83% | 87.97% | NA |
| VI/Aromatic | 96 | 7.30% | 0.00% | 3.12% | 89.58% | NA |
| Intermediate | 90 | 17.80% | 0.00% | 6.67% | 75.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1011329733 | A -> G | LOC_Os10g21950.1 | intron_variant ; MODIFIER | silent_mutation | Average:12.516; most accessible tissue: Minghui63 root, score: 21.615 | N | N | N | N |
| vg1011329733 | A -> DEL | N | N | silent_mutation | Average:12.516; most accessible tissue: Minghui63 root, score: 21.615 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1011329733 | NA | 4.05E-06 | mr1881 | 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 |
| vg1011329733 | 2.44E-06 | 2.44E-06 | mr1877_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 |