| Variant ID: vg0614961169 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 14961169 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 124. )
GTGCCGCATCAGCCTATGCAAGATGGAAATAAAAAATTCAGTAGTTGTCCTATATTATGCAAGATAAATGACATAATTGTTGGAAGTAATACAAATTGGA[C/T]
GTACCGCCACGAAGTAGTCTCGGTCACGGTGCGTGGGATACGCGTCCGTGACAGCGGCAACGTGCGGCTCTGGGGCGTCTGGAGTGAAGGTCACACGCGC
GCGCGTGTGACCTTCACTCCAGACGCCCCAGAGCCGCACGTTGCCGCTGTCACGGACGCGTATCCCACGCACCGTGACCGAGACTACTTCGTGGCGGTAC[G/A]
TCCAATTTGTATTACTTCCAACAATTATGTCATTTATCTTGCATAATATAGGACAACTACTGAATTTTTTATTTCCATCTTGCATAGGCTGATGCGGCAC
| 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 | 27.20% | 0.10% | 7.53% | 65.13% | NA |
| All Indica | 2759 | 2.40% | 0.00% | 4.20% | 93.40% | NA |
| All Japonica | 1512 | 78.00% | 0.30% | 2.51% | 19.18% | NA |
| Aus | 269 | 1.50% | 0.00% | 68.03% | 30.48% | NA |
| Indica I | 595 | 4.70% | 0.00% | 0.67% | 94.62% | NA |
| Indica II | 465 | 0.90% | 0.00% | 0.86% | 98.28% | NA |
| Indica III | 913 | 0.50% | 0.00% | 7.56% | 91.89% | NA |
| Indica Intermediate | 786 | 3.70% | 0.00% | 4.96% | 91.35% | NA |
| Temperate Japonica | 767 | 95.30% | 0.70% | 0.00% | 4.04% | NA |
| Tropical Japonica | 504 | 47.40% | 0.00% | 6.94% | 45.63% | NA |
| Japonica Intermediate | 241 | 86.70% | 0.00% | 1.24% | 12.03% | NA |
| VI/Aromatic | 96 | 9.40% | 0.00% | 12.50% | 78.12% | NA |
| Intermediate | 90 | 32.20% | 0.00% | 7.78% | 60.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0614961169 | C -> T | LOC_Os06g25580.1 | splice_region_variant&intron_variant ; LOW | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0614961169 | C -> DEL | N | N | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |