| Variant ID: vg1001913172 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 1913172 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
ATGTTTTGTATGAGATGCGCAAACATGTTGGTAATCGAGAGGAATTTGACATAAAGGCAAATATAAATCTTGCTCATCTTGATATGTTGGACAAAAGCTC[C/A]
CTATGCTTATTTCTGCACATAACAGTTTTTCAAGTAAACTTACTGCGGAAAAAATGCCTCCGTCCCTCTCCCCTAGCCCCGACACTCACCCGCGGCGGCG
CGCCGCCGCGGGTGAGTGTCGGGGCTAGGGGAGAGGGACGGAGGCATTTTTTCCGCAGTAAGTTTACTTGAAAAACTGTTATGTGCAGAAATAAGCATAG[G/T]
GAGCTTTTGTCCAACATATCAAGATGAGCAAGATTTATATTTGCCTTTATGTCAAATTCCTCTCGATTACCAACATGTTTGCGCATCTCATACAAAACAT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 83.30% | 6.60% | 4.59% | 5.48% | NA |
| All Indica | 2759 | 75.90% | 9.50% | 7.10% | 7.58% | NA |
| All Japonica | 1512 | 99.50% | 0.00% | 0.46% | 0.00% | NA |
| Aus | 269 | 61.30% | 18.60% | 4.46% | 15.61% | NA |
| Indica I | 595 | 57.50% | 19.30% | 20.00% | 3.19% | NA |
| Indica II | 465 | 83.00% | 7.30% | 4.30% | 5.38% | NA |
| Indica III | 913 | 79.50% | 5.10% | 2.30% | 13.03% | NA |
| Indica Intermediate | 786 | 81.30% | 8.30% | 4.58% | 5.85% | NA |
| Temperate Japonica | 767 | 99.20% | 0.00% | 0.78% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 95.80% | 0.00% | 0.00% | 4.17% | NA |
| Intermediate | 90 | 93.30% | 0.00% | 2.22% | 4.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1001913172 | C -> A | LOC_Os10g04130.1 | 5_prime_UTR_variant ; 1051.0bp to feature; MODIFIER | silent_mutation | Average:59.776; most accessible tissue: Callus, score: 84.077 | N | N | N | N |
| vg1001913172 | C -> A | LOC_Os10g04120.1 | upstream_gene_variant ; 3856.0bp to feature; MODIFIER | silent_mutation | Average:59.776; most accessible tissue: Callus, score: 84.077 | N | N | N | N |
| vg1001913172 | C -> DEL | N | N | silent_mutation | Average:59.776; most accessible tissue: Callus, score: 84.077 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1001913172 | 8.89E-07 | 8.87E-07 | mr1473_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 |
| vg1001913172 | 4.01E-06 | 4.01E-06 | mr1473_2 | Ind_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 |
| vg1001913172 | 4.38E-07 | 4.37E-07 | mr1630_2 | 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 |
| vg1001913172 | 1.24E-06 | 1.24E-06 | mr1630_2 | Ind_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 |