| Variant ID: vg0410227364 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 10227364 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CTATGAGTTTTGCGGGAAATCATGGGATGGAAGTAGAAGATCTTAGACGTCCTTTGATGGTTAGTACCCCAAGTAATCAAGCACTCTCTCTGCAACGTAG[T/C]
CCCTCTGTCAGAATAGAAATTCAAGGAGTACCATTTCTGGCCAATCTTATCTTGTTAGAATCCAAAGATCTTGATGTCATCCTAGGGATGGACTGGTTAG
CTAACCAGTCCATCCCTAGGATGACATCAAGATCTTTGGATTCTAACAAGATAAGATTGGCCAGAAATGGTACTCCTTGAATTTCTATTCTGACAGAGGG[A/G]
CTACGTTGCAGAGAGAGTGCTTGATTACTTGGGGTACTAACCATCAAAGGACGTCTAAGATCTTCTACTTCCATCCCATGATTTCCCGCAAAACTCATAG
| 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 | 78.80% | 0.10% | 8.70% | 12.36% | NA |
| All Indica | 2759 | 86.60% | 0.20% | 6.09% | 7.18% | NA |
| All Japonica | 1512 | 63.00% | 0.00% | 13.49% | 23.54% | NA |
| Aus | 269 | 92.90% | 0.40% | 4.46% | 2.23% | NA |
| Indica I | 595 | 93.40% | 0.20% | 3.70% | 2.69% | NA |
| Indica II | 465 | 83.90% | 0.20% | 10.11% | 5.81% | NA |
| Indica III | 913 | 82.60% | 0.30% | 5.91% | 11.17% | NA |
| Indica Intermediate | 786 | 87.50% | 0.00% | 5.73% | 6.74% | NA |
| Temperate Japonica | 767 | 96.90% | 0.00% | 0.52% | 2.61% | NA |
| Tropical Japonica | 504 | 7.70% | 0.00% | 34.92% | 57.34% | NA |
| Japonica Intermediate | 241 | 70.50% | 0.00% | 9.96% | 19.50% | NA |
| VI/Aromatic | 96 | 67.70% | 0.00% | 19.79% | 12.50% | NA |
| Intermediate | 90 | 77.80% | 0.00% | 8.89% | 13.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0410227364 | T -> C | LOC_Os04g18500.1 | synonymous_variant ; p.Ser420Ser; LOW | synonymous_codon | Average:6.883; most accessible tissue: Minghui63 root, score: 13.235 | N | N | N | N |
| vg0410227364 | T -> DEL | LOC_Os04g18500.1 | N | frameshift_variant | Average:6.883; most accessible tissue: Minghui63 root, score: 13.235 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0410227364 | NA | 1.05E-08 | mr1551 | 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 |
| vg0410227364 | NA | 8.27E-10 | mr1580 | 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 |
| vg0410227364 | NA | 1.84E-06 | mr1398_2 | 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 |
| vg0410227364 | 1.13E-06 | NA | mr1509_2 | 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 |