| Variant ID: vg0807399852 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr08 | Position: 7399852 |
| Reference Allele: CATAT | Alternative Allele: CAT,C,CATATAT,CATATATAT |
| Primary Allele: CAT | Secondary Allele: CATAT |
Inferred Ancestral Allele: Not determined.
GGCGTAATGATTGATGACAGTGGGATGACAACTGTTGACCTTAACAAGGTTGGATACTCGGATGAACCTTTTGTCCTTGCCAATGATGTAACGCAAGTAA[CATAT/CAT,C,CATATAT,CATATATAT]
ATATATATATATATGTTACTTCGCATTTATCCTAATACATCTTTTTGTATCTTGCAGAAAAGACGTGTTGTCGGAGTCGTCCGTCAAGCCTGAGTGGAAG
CTTCCACTCAGGCTTGACGGACGACTCCGACAACACGTCTTTTCTGCAAGATACAAAAAGATGTATTAGGATAAATGCGAAGTAACATATATATATATAT[ATATG/ATG,G,ATATATG,ATATATATG]
TTACTTGCGTTACATCATTGGCAAGGACAAAAGGTTCATCCGAGTATCCAACCTTGTTAAGGTCAACAGTTGTCATCCCACTGTCATCAATCATTACGCC
| Populations | Population Size | Frequency of CAT(primary allele) | Frequency of CATAT(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 25.10% | 3.90% | 6.52% | 63.61% | CATATAT: 0.68%; C: 0.13%; CATATATAT: 0.11% |
| All Indica | 2759 | 8.60% | 0.20% | 6.34% | 84.85% | CATATAT: 0.04% |
| All Japonica | 1512 | 60.70% | 11.30% | 7.14% | 18.25% | CATATAT: 1.85%; C: 0.40%; CATATATAT: 0.33% |
| Aus | 269 | 0.40% | 0.40% | 5.95% | 93.31% | NA |
| Indica I | 595 | 22.90% | 0.00% | 13.11% | 64.03% | NA |
| Indica II | 465 | 7.70% | 0.60% | 8.17% | 83.44% | NA |
| Indica III | 913 | 0.40% | 0.20% | 0.77% | 98.47% | CATATAT: 0.11% |
| Indica Intermediate | 786 | 7.80% | 0.00% | 6.62% | 85.62% | NA |
| Temperate Japonica | 767 | 51.10% | 7.80% | 9.00% | 31.68% | CATATAT: 0.26%; C: 0.13% |
| Tropical Japonica | 504 | 72.20% | 15.70% | 3.57% | 3.57% | CATATAT: 4.17%; C: 0.60%; CATATATAT: 0.20% |
| Japonica Intermediate | 241 | 67.20% | 13.30% | 8.71% | 6.22% | CATATAT: 2.07%; CATATATAT: 1.66%; C: 0.83% |
| VI/Aromatic | 96 | 1.00% | 2.10% | 4.17% | 92.71% | NA |
| Intermediate | 90 | 32.20% | 4.40% | 5.56% | 54.44% | CATATAT: 3.33% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0807399852 | CATAT -> CATATAT | LOC_Os08g12500.1 | intron_variant ; MODIFIER | silent_mutation | Average:5.499; most accessible tissue: Minghui63 flower, score: 9.27 | N | N | N | N |
| vg0807399852 | CATAT -> C | LOC_Os08g12500.1 | intron_variant ; MODIFIER | silent_mutation | Average:5.499; most accessible tissue: Minghui63 flower, score: 9.27 | N | N | N | N |
| vg0807399852 | CATAT -> DEL | N | N | silent_mutation | Average:5.499; most accessible tissue: Minghui63 flower, score: 9.27 | N | N | N | N |
| vg0807399852 | CATAT -> CAT | LOC_Os08g12500.1 | intron_variant ; MODIFIER | silent_mutation | Average:5.499; most accessible tissue: Minghui63 flower, score: 9.27 | N | N | N | N |
| vg0807399852 | CATAT -> CATATATAT | LOC_Os08g12500.1 | intron_variant ; MODIFIER | silent_mutation | Average:5.499; most accessible tissue: Minghui63 flower, score: 9.27 | N | N | N | N |