| Variant ID: vg1222999986 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 22999986 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CCATTTCATATTATAAAACTTTGTAACATTATCCATATTCATATATATATTAATGAATCTTTTTTTAGATAATATATGTTAATAAATATAGACACACACA[T/C]
ATATATATATACATATATATATATATACATATATATATATATTATATATATATATATATAATATATATATATATATGTATGTGTGTGTTTAGATTTATTA
TAATAAATCTAAACACACACATACATATATATATATATATTATATATATATATATATAATATATATATATATGTATATATATATATATGTATATATATAT[A/G]
TGTGTGTGTCTATATTTATTAACATATATTATCTAAAAAAAGATTCATTAATATATATATGAATATGGATAATGTTACAAAGTTTTATAATATGAAATGG
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 5.00% | 1.20% | 12.23% | 81.61% | NA |
| All Indica | 2759 | 1.00% | 2.00% | 11.34% | 85.72% | NA |
| All Japonica | 1512 | 10.40% | 0.10% | 12.17% | 77.31% | NA |
| Aus | 269 | 11.50% | 0.40% | 21.93% | 66.17% | NA |
| Indica I | 595 | 1.30% | 0.20% | 3.87% | 94.62% | NA |
| Indica II | 465 | 0.60% | 0.20% | 8.39% | 90.75% | NA |
| Indica III | 913 | 1.40% | 4.50% | 19.61% | 74.48% | NA |
| Indica Intermediate | 786 | 0.40% | 1.40% | 9.16% | 89.06% | NA |
| Temperate Japonica | 767 | 11.70% | 0.00% | 3.39% | 84.88% | NA |
| Tropical Japonica | 504 | 7.70% | 0.20% | 24.40% | 67.66% | NA |
| Japonica Intermediate | 241 | 12.00% | 0.00% | 14.52% | 73.44% | NA |
| VI/Aromatic | 96 | 11.50% | 0.00% | 10.42% | 78.12% | NA |
| Intermediate | 90 | 7.80% | 1.10% | 13.33% | 77.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1222999986 | T -> C | LOC_Os12g37480.1 | 3_prime_UTR_variant ; 272.0bp to feature; MODIFIER | silent_mutation | Average:36.472; most accessible tissue: Callus, score: 65.184 | N | N | N | N |
| vg1222999986 | T -> C | LOC_Os12g37470.1 | upstream_gene_variant ; 1462.0bp to feature; MODIFIER | silent_mutation | Average:36.472; most accessible tissue: Callus, score: 65.184 | N | N | N | N |
| vg1222999986 | T -> C | LOC_Os12g37490.1 | downstream_gene_variant ; 2225.0bp to feature; MODIFIER | silent_mutation | Average:36.472; most accessible tissue: Callus, score: 65.184 | N | N | N | N |
| vg1222999986 | T -> DEL | N | N | silent_mutation | Average:36.472; most accessible tissue: Callus, score: 65.184 | N | N | N | N |