| Variant ID: vg1008612264 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 8612264 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
AGCAAAGAATTGTCGTCGATGGAAGAAGTTGTGTCTCTCCCCGACCTACTCCAGGCCAAGCAAAGGGCGATACCAAGCAGAAGACCGTCATCCGCTTCAA[C/A]
CAGCAATCAGAAGGAAGCTTCTCCTGTGAATGATAGCAATATGCAGTCCTATCACATCATCACAGAACCAATCAAGGATAATGCAGTCACTAGAACCACG
CGTGGTTCTAGTGACTGCATTATCCTTGATTGGTTCTGTGATGATGTGATAGGACTGCATATTGCTATCATTCACAGGAGAAGCTTCCTTCTGATTGCTG[G/T]
TTGAAGCGGATGACGGTCTTCTGCTTGGTATCGCCCTTTGCTTGGCCTGGAGTAGGTCGGGGAGAGACACAACTTCTTCCATCGACGACAATTCTTTGCT
| 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 | 14.60% | 0.00% | 5.04% | 80.28% | NA |
| All Indica | 2759 | 1.00% | 0.00% | 5.55% | 93.44% | NA |
| All Japonica | 1512 | 42.50% | 0.10% | 3.77% | 53.64% | NA |
| Aus | 269 | 0.00% | 0.00% | 0.00% | 100.00% | NA |
| Indica I | 595 | 0.80% | 0.00% | 0.50% | 98.66% | NA |
| Indica II | 465 | 0.90% | 0.00% | 0.65% | 98.49% | NA |
| Indica III | 913 | 0.80% | 0.00% | 12.92% | 86.31% | NA |
| Indica Intermediate | 786 | 1.50% | 0.00% | 3.69% | 94.78% | NA |
| Temperate Japonica | 767 | 59.10% | 0.00% | 1.30% | 39.63% | NA |
| Tropical Japonica | 504 | 8.70% | 0.20% | 8.73% | 82.34% | NA |
| Japonica Intermediate | 241 | 60.20% | 0.40% | 1.24% | 38.17% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 19.79% | 80.21% | NA |
| Intermediate | 90 | 24.40% | 0.00% | 10.00% | 65.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1008612264 | C -> A | LOC_Os10g17150.1 | missense_variant ; p.Asn407Lys; MODERATE | nonsynonymous_codon | Average:4.409; most accessible tissue: Minghui63 panicle, score: 7.125 | unknown | unknown | TOLERATED | 0.15 |
| vg1008612264 | C -> DEL | LOC_Os10g17150.1 | N | frameshift_variant | Average:4.409; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |