| Variant ID: vg0415232460 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 15232460 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TGGATTCTACCATTGACAAGGACTTCACATATGGTTACTTCATATCCAATGGCACCAGTTTTATTCCTTCTCTATCCAACGGTCCCAAATTTCCTGGTGA[C/T]
GTGGCACAATGTGGTAGTGAAAAACTTTACTTTTTTCACTACTTTAGATAAGGGCAAAAACAAAAACCCTAAAAAACATGGCAAAATCAATATTAAACAT
ATGTTTAATATTGATTTTGCCATGTTTTTTAGGGTTTTTGTTTTTGCCCTTATCTAAAGTAGTGAAAAAAGTAAAGTTTTTCACTACCACATTGTGCCAC[G/A]
TCACCAGGAAATTTGGGACCGTTGGATAGAGAAGGAATAAAACTGGTGCCATTGGATATGAAGTAACCATATGTGAAGTCCTTGTCAATGGTAGAATCCA
| 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 | 86.40% | 7.80% | 0.55% | 5.27% | NA |
| All Indica | 2759 | 84.30% | 7.60% | 0.83% | 7.25% | NA |
| All Japonica | 1512 | 88.00% | 9.30% | 0.20% | 2.58% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 74.50% | 24.90% | 0.34% | 0.34% | NA |
| Indica II | 465 | 96.80% | 0.40% | 0.00% | 2.80% | NA |
| Indica III | 913 | 79.70% | 2.80% | 1.86% | 15.55% | NA |
| Indica Intermediate | 786 | 89.70% | 4.30% | 0.51% | 5.47% | NA |
| Temperate Japonica | 767 | 83.40% | 11.90% | 0.39% | 4.30% | NA |
| Tropical Japonica | 504 | 93.10% | 6.70% | 0.00% | 0.20% | NA |
| Japonica Intermediate | 241 | 91.70% | 6.20% | 0.00% | 2.07% | NA |
| VI/Aromatic | 96 | 81.20% | 13.50% | 0.00% | 5.21% | NA |
| Intermediate | 90 | 86.70% | 7.80% | 0.00% | 5.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0415232460 | C -> DEL | N | N | silent_mutation | Average:19.059; most accessible tissue: Zhenshan97 flag leaf, score: 27.583 | N | N | N | N |
| vg0415232460 | C -> T | LOC_Os04g26130.1 | upstream_gene_variant ; 261.0bp to feature; MODIFIER | silent_mutation | Average:19.059; most accessible tissue: Zhenshan97 flag leaf, score: 27.583 | N | N | N | N |
| vg0415232460 | C -> T | LOC_Os04g26130-LOC_Os04g26140 | intergenic_region ; MODIFIER | silent_mutation | Average:19.059; most accessible tissue: Zhenshan97 flag leaf, score: 27.583 | N | N | N | N |