| Variant ID: vg0224432257 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr02 | Position: 24432257 |
| Reference Allele: TA | Alternative Allele: CA,T |
| Primary Allele: CA | Secondary Allele: TA |
Inferred Ancestral Allele: Not determined.
CACAGCTAGCTATACAATACATCTAACACAGACTATGTGATATGGTAATCGTATCACCATCTTTAACAGAAAGCTTACTGTCCGTGTAAGCATCGCCTTT[TA/CA,T]
AAAACACAATTGACTTCATTGCGACATTTGGATCTGTAGTCCAGCACTGATTTTTGTAAAATTCATTGCACTTGGAAAATTCTTGCTGTTGAAAGTCCCA
TGGGACTTTCAACAGCAAGAATTTTCCAAGTGCAATGAATTTTACAAAAATCAGTGCTGGACTACAGATCCAAATGTCGCAATGAAGTCAATTGTGTTTT[TA/TG,A]
AAAGGCGATGCTTACACGGACAGTAAGCTTTCTGTTAAAGATGGTGATACGATTACCATATCACATAGTCTGTGTTAGATGTATTGTATAGCTAGCTGTG
| Populations | Population Size | Frequency of CA(primary allele) | Frequency of TA(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 54.60% | 17.90% | 0.25% | 24.67% | T: 2.56% |
| All Indica | 2759 | 58.10% | 17.40% | 0.29% | 21.31% | T: 2.97% |
| All Japonica | 1512 | 44.70% | 20.00% | 0.26% | 34.46% | T: 0.60% |
| Aus | 269 | 74.00% | 12.60% | 0.00% | 12.64% | T: 0.74% |
| Indica I | 595 | 45.50% | 15.30% | 0.34% | 38.32% | T: 0.50% |
| Indica II | 465 | 76.60% | 15.90% | 0.22% | 3.87% | T: 3.44% |
| Indica III | 913 | 51.60% | 20.00% | 0.33% | 24.97% | T: 3.07% |
| Indica Intermediate | 786 | 64.10% | 16.70% | 0.25% | 14.50% | T: 4.45% |
| Temperate Japonica | 767 | 36.00% | 19.80% | 0.13% | 43.81% | T: 0.26% |
| Tropical Japonica | 504 | 60.10% | 23.60% | 0.40% | 15.87% | NA |
| Japonica Intermediate | 241 | 40.20% | 12.90% | 0.41% | 43.57% | T: 2.90% |
| VI/Aromatic | 96 | 55.20% | 9.40% | 0.00% | 7.29% | T: 28.12% |
| Intermediate | 90 | 57.80% | 23.30% | 0.00% | 17.78% | T: 1.11% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0224432257 | TA -> T | LOC_Os02g40340.1 | frameshift_variant ; p.Leu358fs; HIGH | frameshift_variant | Average:46.873; most accessible tissue: Callus, score: 78.34 | N | N | N | N |
| vg0224432257 | TA -> T | LOC_Os02g40340.2 | frameshift_variant ; p.Leu358fs; HIGH | frameshift_variant | Average:46.873; most accessible tissue: Callus, score: 78.34 | N | N | N | N |
| vg0224432257 | TA -> CA | LOC_Os02g40340.1 | synonymous_variant ; p.Leu358Leu; LOW | synonymous_codon | Average:46.873; most accessible tissue: Callus, score: 78.34 | N | N | N | N |
| vg0224432257 | TA -> CA | LOC_Os02g40340.2 | synonymous_variant ; p.Leu358Leu; LOW | synonymous_codon | Average:46.873; most accessible tissue: Callus, score: 78.34 | N | N | N | N |
| vg0224432257 | TA -> DEL | LOC_Os02g40340.2 | N | frameshift_variant | Average:46.873; most accessible tissue: Callus, score: 78.34 | N | N | N | N |
| vg0224432257 | TA -> DEL | LOC_Os02g40340.1 | N | frameshift_variant | Average:46.873; most accessible tissue: Callus, score: 78.34 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0224432257 | 1.51E-07 | NA | mr1232 | All | YES | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0224432257 | 5.67E-06 | NA | mr1557 | All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0224432257 | 3.74E-06 | NA | mr1557 | Ind_All | YES | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |