| Variant ID: vg1101254918 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 1254918 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GACTTCGTCCGCAAACTAATTCACGTGCTCCAAGTGATGGTACGACAAGAATTTATTTTATTTTCTACATAAAGTACTTAGTATAATTTGTTTTTCAATT[G/A]
TTTTAGGTTCTCAATCAGTTAAGCGCAGTAGCTGTGGCAAAAACAAATGTGAGGACTGCATCGTCTCAAGGAGTAAACTAGTAACAAAATGAAATATTGT
ACAATATTTCATTTTGTTACTAGTTTACTCCTTGAGACGATGCAGTCCTCACATTTGTTTTTGCCACAGCTACTGCGCTTAACTGATTGAGAACCTAAAA[C/T]
AATTGAAAAACAAATTATACTAAGTACTTTATGTAGAAAATAAAATAAATTCTTGTCGTACCATCACTTGGAGCACGTGAATTAGTTTGCGGACGAAGTC
| 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 | 36.70% | 0.20% | 8.08% | 55.01% | NA |
| All Indica | 2759 | 6.30% | 0.00% | 7.00% | 86.66% | NA |
| All Japonica | 1512 | 96.70% | 0.50% | 0.46% | 2.31% | NA |
| Aus | 269 | 7.80% | 0.00% | 57.62% | 34.57% | NA |
| Indica I | 595 | 6.40% | 0.00% | 10.25% | 83.36% | NA |
| Indica II | 465 | 6.00% | 0.00% | 1.51% | 92.47% | NA |
| Indica III | 913 | 1.90% | 0.00% | 6.57% | 91.57% | NA |
| Indica Intermediate | 786 | 11.70% | 0.00% | 8.27% | 80.03% | NA |
| Temperate Japonica | 767 | 96.60% | 0.90% | 0.65% | 1.83% | NA |
| Tropical Japonica | 504 | 97.20% | 0.20% | 0.20% | 2.38% | NA |
| Japonica Intermediate | 241 | 95.90% | 0.00% | 0.41% | 3.73% | NA |
| VI/Aromatic | 96 | 33.30% | 0.00% | 22.92% | 43.75% | NA |
| Intermediate | 90 | 51.10% | 0.00% | 5.56% | 43.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1101254918 | G -> A | LOC_Os11g03340.1 | splice_region_variant&intron_variant ; LOW | silent_mutation | Average:4.415; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1101254918 | G -> A | LOC_Os11g03330.1 | downstream_gene_variant ; 938.0bp to feature; MODIFIER | silent_mutation | Average:4.415; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1101254918 | G -> DEL | N | N | silent_mutation | Average:4.415; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |