| Variant ID: vg0320045406 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 20045406 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GATTTTTTACCAAAAACCGACTCAAGGACCTCAATGTAAGGTCAAAGGGACTCAAATGTAAATATGAAAATTACAGGGACTCAACTGTAGAAGTCCAAAC[C/T]
AAAATTAAAAATTATACAAAAATGGAATGCTCAAGTTATGTCGGTTCCGTTTTTGCAAACGGATCTTGAATCGACACCAAAATAAAATTTCATCGAAGTT
AACTTCGATGAAATTTTATTTTGGTGTCGATTCAAGATCCGTTTGCAAAAACGGAACCGACATAACTTGAGCATTCCATTTTTGTATAATTTTTAATTTT[G/A]
GTTTGGACTTCTACAGTTGAGTCCCTGTAATTTTCATATTTACATTTGAGTCCCTTTGACCTTACATTGAGGTCCTTGAGTCGGTTTTTGGTAAAAAATC
| 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 | 71.70% | 2.40% | 22.89% | 3.05% | NA |
| All Indica | 2759 | 58.40% | 4.00% | 36.10% | 1.52% | NA |
| All Japonica | 1512 | 89.70% | 0.10% | 3.70% | 6.55% | NA |
| Aus | 269 | 95.50% | 0.00% | 4.46% | 0.00% | NA |
| Indica I | 595 | 46.60% | 2.50% | 49.08% | 1.85% | NA |
| Indica II | 465 | 44.30% | 4.30% | 48.82% | 2.58% | NA |
| Indica III | 913 | 74.30% | 4.40% | 20.37% | 0.99% | NA |
| Indica Intermediate | 786 | 57.40% | 4.30% | 37.02% | 1.27% | NA |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 75.60% | 0.20% | 9.52% | 14.68% | NA |
| Japonica Intermediate | 241 | 86.70% | 0.00% | 2.90% | 10.37% | NA |
| VI/Aromatic | 96 | 96.90% | 1.00% | 2.08% | 0.00% | NA |
| Intermediate | 90 | 77.80% | 1.10% | 17.78% | 3.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0320045406 | C -> T | LOC_Os03g36130.1 | 5_prime_UTR_variant ; 689.0bp to feature; MODIFIER | silent_mutation | Average:14.526; most accessible tissue: Minghui63 root, score: 25.504 | N | N | N | N |
| vg0320045406 | C -> T | LOC_Os03g36120.1 | downstream_gene_variant ; 4221.0bp to feature; MODIFIER | silent_mutation | Average:14.526; most accessible tissue: Minghui63 root, score: 25.504 | N | N | N | N |
| vg0320045406 | C -> T | LOC_Os03g36140.1 | downstream_gene_variant ; 3833.0bp to feature; MODIFIER | silent_mutation | Average:14.526; most accessible tissue: Minghui63 root, score: 25.504 | N | N | N | N |
| vg0320045406 | C -> DEL | N | N | silent_mutation | Average:14.526; most accessible tissue: Minghui63 root, score: 25.504 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0320045406 | 4.41E-06 | 4.41E-06 | mr1361 | Ind_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 |