| Variant ID: vg1222999944 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr12 | Position: 22999944 |
| Reference Allele: CT | Alternative Allele: C |
| Primary Allele: CT | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
AAGGATGGATTTGATACACGGTCATCATAATAATTACTTCCTCCATTTCATATTATAAAACTTTGTAACATTATCCATATTCATATATATATTAATGAAT[CT/C]
TTTTTTAGATAATATATGTTAATAAATATAGACACACACATATATATATATACATATATATATATATACATATATATATATATTATATATATATATATAT
ATATATATATATATATAATATATATATATATGTATATATATATATATGTATATATATATATGTGTGTGTCTATATTTATTAACATATATTATCTAAAAAA[AG/G]
ATTCATTAATATATATATGAATATGGATAATGTTACAAAGTTTTATAATATGAAATGGAGGAAGTAATTATTATGATGACCGTGTATCAAATCCATCCTT
| Populations | Population Size | Frequency of CT(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 12.10% | 5.70% | 12.40% | 69.78% | NA |
| All Indica | 2759 | 6.70% | 9.40% | 11.89% | 71.98% | NA |
| All Japonica | 1512 | 21.10% | 0.30% | 11.38% | 67.26% | NA |
| Aus | 269 | 15.20% | 0.40% | 20.82% | 63.57% | NA |
| Indica I | 595 | 8.70% | 1.00% | 8.40% | 81.85% | NA |
| Indica II | 465 | 1.30% | 1.70% | 9.89% | 87.10% | NA |
| Indica III | 913 | 5.10% | 22.10% | 15.99% | 56.74% | NA |
| Indica Intermediate | 786 | 10.20% | 5.60% | 10.94% | 73.28% | NA |
| Temperate Japonica | 767 | 16.80% | 0.00% | 6.26% | 76.92% | NA |
| Tropical Japonica | 504 | 25.40% | 0.80% | 18.45% | 55.36% | NA |
| Japonica Intermediate | 241 | 25.70% | 0.00% | 12.86% | 61.41% | NA |
| VI/Aromatic | 96 | 13.50% | 1.00% | 14.58% | 70.83% | NA |
| Intermediate | 90 | 16.70% | 3.30% | 17.78% | 62.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1222999944 | CT -> C | LOC_Os12g37480.1 | 3_prime_UTR_variant ; 313.0bp to feature; MODIFIER | silent_mutation | Average:34.032; most accessible tissue: Callus, score: 65.184 | N | N | N | N |
| vg1222999944 | CT -> C | LOC_Os12g37470.1 | upstream_gene_variant ; 1421.0bp to feature; MODIFIER | silent_mutation | Average:34.032; most accessible tissue: Callus, score: 65.184 | N | N | N | N |
| vg1222999944 | CT -> C | LOC_Os12g37490.1 | downstream_gene_variant ; 2266.0bp to feature; MODIFIER | silent_mutation | Average:34.032; most accessible tissue: Callus, score: 65.184 | N | N | N | N |
| vg1222999944 | CT -> DEL | N | N | silent_mutation | Average:34.032; most accessible tissue: Callus, score: 65.184 | N | N | N | N |