| Variant ID: vg1222999919 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 22999919 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CTTCCACTAACATTTGTGAGGTGTGAAGGATGGATTTGATACACGGTCATCATAATAATTACTTCCTCCATTTCATATTATAAAACTTTGTAACATTATC[C/A]
ATATTCATATATATATTAATGAATCTTTTTTTAGATAATATATGTTAATAAATATAGACACACACATATATATATATACATATATATATATATACATATA
TATATGTATATATATATATATGTATATATATATATGTGTGTGTCTATATTTATTAACATATATTATCTAAAAAAAGATTCATTAATATATATATGAATAT[G/T]
GATAATGTTACAAAGTTTTATAATATGAAATGGAGGAAGTAATTATTATGATGACCGTGTATCAAATCCATCCTTCACACCTCACAAATGTTAGTGGAAG
| 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 | 43.30% | 0.20% | 11.74% | 44.69% | NA |
| All Indica | 2759 | 47.70% | 0.30% | 7.58% | 44.47% | NA |
| All Japonica | 1512 | 39.30% | 0.00% | 11.31% | 49.40% | NA |
| Aus | 269 | 25.30% | 1.50% | 53.53% | 19.70% | NA |
| Indica I | 595 | 26.70% | 0.00% | 15.46% | 57.82% | NA |
| Indica II | 465 | 51.00% | 0.20% | 3.01% | 45.81% | NA |
| Indica III | 913 | 59.30% | 0.30% | 5.48% | 34.94% | NA |
| Indica Intermediate | 786 | 48.20% | 0.40% | 6.74% | 44.66% | NA |
| Temperate Japonica | 767 | 28.20% | 0.00% | 11.34% | 60.50% | NA |
| Tropical Japonica | 504 | 53.60% | 0.00% | 11.51% | 34.92% | NA |
| Japonica Intermediate | 241 | 44.80% | 0.00% | 10.79% | 44.40% | NA |
| VI/Aromatic | 96 | 33.30% | 0.00% | 17.71% | 48.96% | NA |
| Intermediate | 90 | 42.20% | 0.00% | 15.56% | 42.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1222999919 | C -> DEL | N | N | silent_mutation | Average:30.836; most accessible tissue: Zhenshan97 flower, score: 49.964 | N | N | N | N |
| vg1222999919 | C -> A | LOC_Os12g37480.1 | 3_prime_UTR_variant ; 339.0bp to feature; MODIFIER | silent_mutation | Average:30.836; most accessible tissue: Zhenshan97 flower, score: 49.964 | N | N | N | N |
| vg1222999919 | C -> A | LOC_Os12g37470.1 | upstream_gene_variant ; 1395.0bp to feature; MODIFIER | silent_mutation | Average:30.836; most accessible tissue: Zhenshan97 flower, score: 49.964 | N | N | N | N |
| vg1222999919 | C -> A | LOC_Os12g37490.1 | downstream_gene_variant ; 2292.0bp to feature; MODIFIER | silent_mutation | Average:30.836; most accessible tissue: Zhenshan97 flower, score: 49.964 | N | N | N | N |