| Variant ID: vg0903406707 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr09 | Position: 3406707 |
| Reference Allele: CA | Alternative Allele: C,GA |
| Primary Allele: CA | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
AATTATTTATATTGTGAGTATTATTAAAATATGCAATAGATCAAAACTGGGGTATTGTTTTATATCAAAGTCAAGTACATAATATCTGTCTCGCATATGT[CA/C,GA]
AATAATACAGTGCTGTAGGAAAAAAACAGAGATGGAGAGTTGGATACATACCACAAATTAGATCCTACCATTGGTTTAGCAAGGTCTCCATATTTACCAG
CTGGTAAATATGGAGACCTTGCTAAACCAATGGTAGGATCTAATTTGTGGTATGTATCCAACTCTCCATCTCTGTTTTTTTCCTACAGCACTGTATTATT[TG/G,TC]
ACATATGCGAGACAGATATTATGTACTTGACTTTGATATAAAACAATACCCCAGTTTTGATCTATTGCATATTTTAATAATACTCACAATATAAATAATT
| Populations | Population Size | Frequency of CA(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.30% | 0.70% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 75.00% | 25.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 94.40% | 5.60% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0903406707 | CA -> GA | LOC_Os09g07010.1 | upstream_gene_variant ; 3598.0bp to feature; MODIFIER | N | Average:48.907; most accessible tissue: Callus, score: 78.358 | N | N | N | N |
| vg0903406707 | CA -> GA | LOC_Os09g07030.1 | downstream_gene_variant ; 2173.0bp to feature; MODIFIER | N | Average:48.907; most accessible tissue: Callus, score: 78.358 | N | N | N | N |
| vg0903406707 | CA -> GA | LOC_Os09g07020.1 | intron_variant ; MODIFIER | N | Average:48.907; most accessible tissue: Callus, score: 78.358 | N | N | N | N |
| vg0903406707 | CA -> GA | LOC_Os09g07020.2 | intron_variant ; MODIFIER | N | Average:48.907; most accessible tissue: Callus, score: 78.358 | N | N | N | N |
| vg0903406707 | CA -> C | LOC_Os09g07010.1 | upstream_gene_variant ; 3599.0bp to feature; MODIFIER | silent_mutation | Average:48.907; most accessible tissue: Callus, score: 78.358 | N | N | N | N |
| vg0903406707 | CA -> C | LOC_Os09g07030.1 | downstream_gene_variant ; 2172.0bp to feature; MODIFIER | silent_mutation | Average:48.907; most accessible tissue: Callus, score: 78.358 | N | N | N | N |
| vg0903406707 | CA -> C | LOC_Os09g07020.1 | intron_variant ; MODIFIER | silent_mutation | Average:48.907; most accessible tissue: Callus, score: 78.358 | N | N | N | N |
| vg0903406707 | CA -> C | LOC_Os09g07020.2 | intron_variant ; MODIFIER | silent_mutation | Average:48.907; most accessible tissue: Callus, score: 78.358 | N | N | N | N |