| Variant ID: vg0317761620 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 17761620 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 92. )
CCGGTCTCTAAACTTGTACCGTTGTGTCATTCCGGTCCCTAAACTCGCAAATCGACCGTTTAGGTTCTCAAACTTGTTCGACTGTGTCATCCCGATCTCT[A/C]
AACTGTTGGAAATATAGTCATTAATCGGCATATTTTAATCCAAGAAAATGAAACAATGATCATGGCATAAGCAGTGTAGGGTGATCTTAACATAACCAGT
ACTGGTTATGTTAAGATCACCCTACACTGCTTATGCCATGATCATTGTTTCATTTTCTTGGATTAAAATATGCCGATTAATGACTATATTTCCAACAGTT[T/G]
AGAGATCGGGATGACACAGTCGAACAAGTTTGAGAACCTAAACGGTCGATTTGCGAGTTTAGGGACCGGAATGACACAACGGTACAAGTTTAGAGACCGG
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 34.00% | 0.50% | 1.23% | 64.28% | NA |
| All Indica | 2759 | 6.80% | 0.00% | 0.72% | 92.46% | NA |
| All Japonica | 1512 | 85.10% | 1.50% | 0.73% | 12.70% | NA |
| Aus | 269 | 2.60% | 0.00% | 8.55% | 88.85% | NA |
| Indica I | 595 | 5.70% | 0.00% | 0.34% | 93.95% | NA |
| Indica II | 465 | 7.50% | 0.00% | 0.65% | 91.83% | NA |
| Indica III | 913 | 6.40% | 0.00% | 1.42% | 92.22% | NA |
| Indica Intermediate | 786 | 7.60% | 0.10% | 0.25% | 91.98% | NA |
| Temperate Japonica | 767 | 99.70% | 0.00% | 0.00% | 0.26% | NA |
| Tropical Japonica | 504 | 63.30% | 3.60% | 1.98% | 31.15% | NA |
| Japonica Intermediate | 241 | 83.80% | 2.10% | 0.41% | 13.69% | NA |
| VI/Aromatic | 96 | 84.40% | 0.00% | 3.12% | 12.50% | NA |
| Intermediate | 90 | 50.00% | 0.00% | 1.11% | 48.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0317761620 | A -> C | LOC_Os03g31190.1 | stop_lost&splice_region_variant ; p.Ter150Gluext*?; HIGH | stop_lost | Average:35.807; most accessible tissue: Minghui63 panicle, score: 59.629 | N | N | N | N |
| vg0317761620 | A -> DEL | LOC_Os03g31190.1 | N | frameshift_variant | Average:35.807; most accessible tissue: Minghui63 panicle, score: 59.629 | N | N | N | N |