| Variant ID: vg1114871222 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr11 | Position: 14871222 |
| Reference Allele: T | Alternative Allele: C,TGTGTCACGTCCCAAAAC |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.03, others allele: 0.00, population size: 115. )
CGGCTGGCAAGGAGATTCAGCCAGAAAAGACCGTGCCGCAGGAGTACTGCAACACGCGGTTGCTGCCGTTTCCCCAACGAATGAGGAAACCGTCAGTGGA[T/C,TGTGTCACGTCCCAAAAC]
GAGCAGTTTGCTCGTTTTGTTGAAGTAATCCAAAAGATCCACATCAACGTGCCATTGTTGGATGCTATGCAAGTGCCGACATACGCCCATTATCTCAAGG
CCTTGAGATAATGGGCGTATGTCGGCACTTGCATAGCATCCAACAATGGCACGTTGATGTGGATCTTTTGGATTACTTCAACAAAACGAGCAAACTGCTC[A/G,GTTTTGGGACGTGACACA]
TCCACTGACGGTTTCCTCATTCGTTGGGGAAACGGCAGCAACCGCGTGTTGCAGTACTCCTGCGGCACGGTCTTTTCTGGCTGAATCTCCTTGCCAGCCG
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 67.70% | 8.50% | 19.85% | 2.58% | TGTGTCACGTCCCAAAAC: 1.40% |
| All Indica | 2759 | 61.80% | 1.40% | 30.41% | 3.99% | TGTGTCACGTCCCAAAAC: 2.39% |
| All Japonica | 1512 | 75.90% | 22.50% | 1.06% | 0.53% | NA |
| Aus | 269 | 73.60% | 3.30% | 23.05% | 0.00% | NA |
| Indica I | 595 | 46.60% | 1.30% | 43.70% | 7.06% | TGTGTCACGTCCCAAAAC: 1.34% |
| Indica II | 465 | 60.00% | 0.20% | 35.27% | 3.87% | TGTGTCACGTCCCAAAAC: 0.65% |
| Indica III | 913 | 73.20% | 0.20% | 20.81% | 1.53% | TGTGTCACGTCCCAAAAC: 4.27% |
| Indica Intermediate | 786 | 61.20% | 3.60% | 28.63% | 4.58% | TGTGTCACGTCCCAAAAC: 2.04% |
| Temperate Japonica | 767 | 61.90% | 36.10% | 1.56% | 0.39% | NA |
| Tropical Japonica | 504 | 97.20% | 1.20% | 0.60% | 0.99% | NA |
| Japonica Intermediate | 241 | 75.90% | 23.70% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 90.60% | 6.20% | 3.12% | 0.00% | NA |
| Intermediate | 90 | 68.90% | 6.70% | 20.00% | 4.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1114871222 | T -> C | LOC_Os11g26000.1 | synonymous_variant ; p.Asp390Asp; LOW | synonymous_codon | Average:13.144; most accessible tissue: Callus, score: 40.69 | N | N | N | N |
| vg1114871222 | T -> DEL | LOC_Os11g26000.1 | N | frameshift_variant | Average:13.144; most accessible tissue: Callus, score: 40.69 | N | N | N | N |
| vg1114871222 | T -> TGTGTCACGTCCCAAAAC | LOC_Os11g26000.1 | frameshift_variant ; p.Glu391fs; HIGH | frameshift_variant | Average:13.144; most accessible tissue: Callus, score: 40.69 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1114871222 | NA | 7.09E-06 | mr1230 | 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 |
| vg1114871222 | NA | 2.42E-06 | mr1345 | 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 |
| vg1114871222 | NA | 4.61E-08 | mr1382 | 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 |
| vg1114871222 | NA | 4.00E-06 | mr1382 | Jap_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 |
| vg1114871222 | NA | 8.70E-06 | mr1424 | 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 |
| vg1114871222 | 9.77E-06 | 9.76E-06 | mr1424 | Jap_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 |
| vg1114871222 | 1.84E-06 | NA | mr1604 | 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 |
| vg1114871222 | 6.81E-06 | NA | mr1810 | 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 |
| vg1114871222 | 6.65E-06 | NA | mr1886 | 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 |