| Variant ID: vg1000028798 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 28798 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CAAAAAGAGAGGACGATGAGATGACGACTCAAGCGAAGGGCGTGGAGGAGGATAGCCATAGCCATGGCCATATCCAAAGAAGTCGAAGTCGGAAGGCAAC[C/T]
CGGCAAAAGGATCCTCAATCTCTTCATCCTCTGGCTCATCGGGCTCGGCCTCGAAACCTGGAGGAGAAGGAGGGATATCAATGTGGTGGTCCTCATAATA
TATTATGAGGACCACCACATTGATATCCCTCCTTCTCCTCCAGGTTTCGAGGCCGAGCCCGATGAGCCAGAGGATGAAGAGATTGAGGATCCTTTTGCCG[G/A]
GTTGCCTTCCGACTTCGACTTCTTTGGATATGGCCATGGCTATGGCTATCCTCCTCCACGCCCTTCGCTTGAGTCGTCATCTCATCGTCCTCTCTTTTTG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 21.00% | 1.40% | 21.10% | 56.56% | NA |
| All Indica | 2759 | 3.00% | 0.70% | 28.78% | 67.52% | NA |
| All Japonica | 1512 | 57.20% | 2.10% | 6.81% | 33.93% | NA |
| Aus | 269 | 3.00% | 1.10% | 27.14% | 68.77% | NA |
| Indica I | 595 | 3.00% | 1.70% | 12.61% | 82.69% | NA |
| Indica II | 465 | 3.40% | 0.00% | 28.17% | 68.39% | NA |
| Indica III | 913 | 2.20% | 0.10% | 42.83% | 54.87% | NA |
| Indica Intermediate | 786 | 3.60% | 1.10% | 25.06% | 70.23% | NA |
| Temperate Japonica | 767 | 87.20% | 0.70% | 1.83% | 10.30% | NA |
| Tropical Japonica | 504 | 14.90% | 4.20% | 13.69% | 67.26% | NA |
| Japonica Intermediate | 241 | 50.20% | 2.10% | 8.30% | 39.42% | NA |
| VI/Aromatic | 96 | 11.50% | 8.30% | 12.50% | 67.71% | NA |
| Intermediate | 90 | 27.80% | 3.30% | 16.67% | 52.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1000028798 | C -> T | LOC_Os10g01020.1 | missense_variant ; p.Gly1956Glu; MODERATE | nonsynonymous_codon ; G1956E | Average:13.302; most accessible tissue: Callus, score: 36.453 | unknown | unknown | DELETERIOUS | 0.02 |
| vg1000028798 | C -> DEL | LOC_Os10g01020.1 | N | frameshift_variant | Average:13.302; most accessible tissue: Callus, score: 36.453 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1000028798 | NA | 2.51E-07 | mr1229 | 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 |
| vg1000028798 | 4.84E-06 | NA | mr1129_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 |
| vg1000028798 | 7.93E-07 | NA | mr1291_2 | Jap_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 |
| vg1000028798 | 1.92E-06 | 1.61E-07 | mr1698_2 | Jap_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 |