| Variant ID: vg0317761631 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 17761631 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
ACTTGTACCGTTGTGTCATTCCGGTCCCTAAACTCGCAAATCGACCGTTTAGGTTCTCAAACTTGTTCGACTGTGTCATCCCGATCTCTAAACTGTTGGA[A/G]
ATATAGTCATTAATCGGCATATTTTAATCCAAGAAAATGAAACAATGATCATGGCATAAGCAGTGTAGGGTGATCTTAACATAACCAGTAGCATACTATG
CATAGTATGCTACTGGTTATGTTAAGATCACCCTACACTGCTTATGCCATGATCATTGTTTCATTTTCTTGGATTAAAATATGCCGATTAATGACTATAT[T/C]
TCCAACAGTTTAGAGATCGGGATGACACAGTCGAACAAGTTTGAGAACCTAAACGGTCGATTTGCGAGTTTAGGGACCGGAATGACACAACGGTACAAGT
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 33.50% | 1.50% | 4.68% | 60.37% | NA |
| All Indica | 2759 | 5.90% | 2.20% | 6.31% | 85.57% | NA |
| All Japonica | 1512 | 85.10% | 0.20% | 0.60% | 14.15% | NA |
| Aus | 269 | 2.60% | 1.50% | 10.41% | 85.50% | NA |
| Indica I | 595 | 4.70% | 0.00% | 4.20% | 91.09% | NA |
| Indica II | 465 | 7.10% | 2.40% | 4.09% | 86.45% | NA |
| Indica III | 913 | 5.50% | 3.50% | 9.09% | 81.93% | NA |
| Indica Intermediate | 786 | 6.70% | 2.20% | 5.98% | 85.11% | NA |
| Temperate Japonica | 767 | 99.70% | 0.00% | 0.00% | 0.26% | NA |
| Tropical Japonica | 504 | 63.30% | 0.40% | 1.39% | 34.92% | NA |
| Japonica Intermediate | 241 | 83.80% | 0.40% | 0.83% | 14.94% | NA |
| VI/Aromatic | 96 | 83.30% | 2.10% | 5.21% | 9.38% | NA |
| Intermediate | 90 | 50.00% | 1.10% | 5.56% | 43.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0317761631 | A -> DEL | LOC_Os03g31190.1 | N | frameshift_variant | Average:34.815; most accessible tissue: Minghui63 panicle, score: 59.629 | N | N | N | N |
| vg0317761631 | A -> G | LOC_Os03g31190.1 | missense_variant ; p.Phe146Ser; MODERATE | nonsynonymous_codon ; F146S | Average:34.815; most accessible tissue: Minghui63 panicle, score: 59.629 | unknown | unknown | DELETERIOUS | 0.00 |