| Variant ID: vg1222999887 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr12 | Position: 22999887 |
| Reference Allele: C | Alternative Allele: T,CTCT |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.03, others allele: 0.00, population size: 73. )
CAATACATGAACACACAAACATAATCAAGACGCTTCCACTAACATTTGTGAGGTGTGAAGGATGGATTTGATACACGGTCATCATAATAATTACTTCCTC[C/T,CTCT]
ATTTCATATTATAAAACTTTGTAACATTATCCATATTCATATATATATTAATGAATCTTTTTTTAGATAATATATGTTAATAAATATAGACACACACATA
TATGTGTGTGTCTATATTTATTAACATATATTATCTAAAAAAAGATTCATTAATATATATATGAATATGGATAATGTTACAAAGTTTTATAATATGAAAT[G/A,AGAG]
GAGGAAGTAATTATTATGATGACCGTGTATCAAATCCATCCTTCACACCTCACAAATGTTAGTGGAAGCGTCTTGATTATGTTTGTGTGTTCATGTATTG
| 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 | 21.40% | 13.00% | 10.22% | 55.25% | CTCT: 0.17% |
| All Indica | 2759 | 17.40% | 21.70% | 10.33% | 50.56% | CTCT: 0.07% |
| All Japonica | 1512 | 29.40% | 0.40% | 7.41% | 62.76% | NA |
| Aus | 269 | 17.50% | 0.40% | 21.93% | 57.99% | CTCT: 2.23% |
| Indica I | 595 | 11.40% | 10.40% | 8.91% | 69.24% | NA |
| Indica II | 465 | 38.10% | 5.20% | 8.39% | 48.39% | NA |
| Indica III | 913 | 6.60% | 40.00% | 13.36% | 39.87% | CTCT: 0.22% |
| Indica Intermediate | 786 | 22.10% | 18.70% | 9.03% | 50.13% | NA |
| Temperate Japonica | 767 | 24.50% | 0.00% | 2.35% | 73.14% | NA |
| Tropical Japonica | 504 | 33.90% | 1.20% | 15.87% | 49.01% | NA |
| Japonica Intermediate | 241 | 35.70% | 0.00% | 5.81% | 58.51% | NA |
| VI/Aromatic | 96 | 16.70% | 1.00% | 18.75% | 63.54% | NA |
| Intermediate | 90 | 26.70% | 7.80% | 10.00% | 55.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1222999887 | C -> CTCT | LOC_Os12g37480.1 | 3_prime_UTR_variant ; 370.0bp to feature; MODIFIER | silent_mutation | Average:28.694; most accessible tissue: Zhenshan97 flower, score: 45.068 | N | N | N | N |
| vg1222999887 | C -> CTCT | LOC_Os12g37470.1 | upstream_gene_variant ; 1364.0bp to feature; MODIFIER | silent_mutation | Average:28.694; most accessible tissue: Zhenshan97 flower, score: 45.068 | N | N | N | N |
| vg1222999887 | C -> CTCT | LOC_Os12g37490.1 | downstream_gene_variant ; 2323.0bp to feature; MODIFIER | silent_mutation | Average:28.694; most accessible tissue: Zhenshan97 flower, score: 45.068 | N | N | N | N |
| vg1222999887 | C -> DEL | N | N | silent_mutation | Average:28.694; most accessible tissue: Zhenshan97 flower, score: 45.068 | N | N | N | N |
| vg1222999887 | C -> T | LOC_Os12g37480.1 | 3_prime_UTR_variant ; 371.0bp to feature; MODIFIER | silent_mutation | Average:28.694; most accessible tissue: Zhenshan97 flower, score: 45.068 | N | N | N | N |
| vg1222999887 | C -> T | LOC_Os12g37470.1 | upstream_gene_variant ; 1363.0bp to feature; MODIFIER | silent_mutation | Average:28.694; most accessible tissue: Zhenshan97 flower, score: 45.068 | N | N | N | N |
| vg1222999887 | C -> T | LOC_Os12g37490.1 | downstream_gene_variant ; 2324.0bp to feature; MODIFIER | silent_mutation | Average:28.694; most accessible tissue: Zhenshan97 flower, score: 45.068 | N | N | N | N |