| Variant ID: vg1222999908 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 22999908 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TAATCAAGACGCTTCCACTAACATTTGTGAGGTGTGAAGGATGGATTTGATACACGGTCATCATAATAATTACTTCCTCCATTTCATATTATAAAACTTT[G/A]
TAACATTATCCATATTCATATATATATTAATGAATCTTTTTTTAGATAATATATGTTAATAAATATAGACACACACATATATATATATACATATATATAT
ATATATATATGTATATATATATATGTGTGTGTCTATATTTATTAACATATATTATCTAAAAAAAGATTCATTAATATATATATGAATATGGATAATGTTA[C/T]
AAAGTTTTATAATATGAAATGGAGGAAGTAATTATTATGATGACCGTGTATCAAATCCATCCTTCACACCTCACAAATGTTAGTGGAAGCGTCTTGATTA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 41.00% | 0.50% | 13.56% | 44.92% | NA |
| All Indica | 2759 | 43.30% | 0.70% | 11.56% | 44.51% | NA |
| All Japonica | 1512 | 39.90% | 0.00% | 10.32% | 49.74% | NA |
| Aus | 269 | 26.00% | 1.90% | 51.30% | 20.82% | NA |
| Indica I | 595 | 27.10% | 0.00% | 14.62% | 58.32% | NA |
| Indica II | 465 | 32.30% | 1.10% | 21.29% | 45.38% | NA |
| Indica III | 913 | 58.90% | 0.30% | 5.37% | 35.38% | NA |
| Indica Intermediate | 786 | 43.90% | 1.30% | 10.69% | 44.15% | NA |
| Temperate Japonica | 767 | 27.60% | 0.00% | 11.73% | 60.63% | NA |
| Tropical Japonica | 504 | 55.20% | 0.00% | 9.33% | 35.52% | NA |
| Japonica Intermediate | 241 | 47.30% | 0.00% | 7.88% | 44.81% | NA |
| VI/Aromatic | 96 | 34.40% | 0.00% | 14.58% | 51.04% | NA |
| Intermediate | 90 | 40.00% | 2.20% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1222999908 | G -> DEL | N | N | silent_mutation | Average:29.24; most accessible tissue: Zhenshan97 flower, score: 44.193 | N | N | N | N |
| vg1222999908 | G -> A | LOC_Os12g37480.1 | 3_prime_UTR_variant ; 350.0bp to feature; MODIFIER | silent_mutation | Average:29.24; most accessible tissue: Zhenshan97 flower, score: 44.193 | N | N | N | N |
| vg1222999908 | G -> A | LOC_Os12g37470.1 | upstream_gene_variant ; 1384.0bp to feature; MODIFIER | silent_mutation | Average:29.24; most accessible tissue: Zhenshan97 flower, score: 44.193 | N | N | N | N |
| vg1222999908 | G -> A | LOC_Os12g37490.1 | downstream_gene_variant ; 2303.0bp to feature; MODIFIER | silent_mutation | Average:29.24; most accessible tissue: Zhenshan97 flower, score: 44.193 | N | N | N | N |