| Variant ID: vg0306599712 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 6599712 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AATCCGGAGAAGGTAATGCAATGCACAAAACTCCCTCTTCGCATGGAGGTAATGATACCCACAAGCCTATATCAGTTTTTCATTTTCATTCATAACCAAC[C/T]
ACATGCACATAATATGTCTCACTCTTACTGTTCTGTCTCATAATAGGTTACCAACAAACTAAACTTAGTAGTTTCTCTCCGTACTCTATGTTGAAAGAGA
TCTCTTTCAACATAGAGTACGGAGAGAAACTACTAAGTTTAGTTTGTTGGTAACCTATTATGAGACAGAACAGTAAGAGTGAGACATATTATGTGCATGT[G/A]
GTTGGTTATGAATGAAAATGAAAAACTGATATAGGCTTGTGGGTATCATTACCTCCATGCGAAGAGGGAGTTTTGTGCATTGCATTACCTTCTCCGGATT
| 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 | 32.00% | 0.70% | 18.18% | 49.13% | NA |
| All Indica | 2759 | 1.60% | 0.00% | 25.08% | 73.32% | NA |
| All Japonica | 1512 | 93.30% | 2.20% | 1.19% | 3.37% | NA |
| Aus | 269 | 0.70% | 0.00% | 24.16% | 75.09% | NA |
| Indica I | 595 | 1.20% | 0.00% | 23.70% | 75.13% | NA |
| Indica II | 465 | 2.60% | 0.00% | 18.49% | 78.92% | NA |
| Indica III | 913 | 0.80% | 0.00% | 33.41% | 65.83% | NA |
| Indica Intermediate | 786 | 2.30% | 0.00% | 20.36% | 77.35% | NA |
| Temperate Japonica | 767 | 96.90% | 0.00% | 0.39% | 2.74% | NA |
| Tropical Japonica | 504 | 85.50% | 6.50% | 2.38% | 5.56% | NA |
| Japonica Intermediate | 241 | 97.90% | 0.00% | 1.24% | 0.83% | NA |
| VI/Aromatic | 96 | 11.50% | 0.00% | 69.79% | 18.75% | NA |
| Intermediate | 90 | 50.00% | 0.00% | 18.89% | 31.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0306599712 | C -> T | LOC_Os03g12490.1 | downstream_gene_variant ; 2451.0bp to feature; MODIFIER | silent_mutation | Average:4.407; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0306599712 | C -> T | LOC_Os03g12480.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.407; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0306599712 | C -> DEL | N | N | silent_mutation | Average:4.407; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |