| Variant ID: vg0218320998 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 18320998 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
ACGCACGAAACATACGGTTTGGTTTGAGTACGGATGGCATGAACCCTTTTGGAGAGATGAGCAGCGGCCATAGCACTTGGCCCATTACGATGTGTATCTA[C/T]
AACCTCCCCCCATGGCTATGCATGAAGAGGAAGTACATAATGATGCCGATTATTATTCAAGGCCCCAAGCAACCTGGTAACGACATCGATGTGTACCTAA
TTAGGTACACATCGATGTCGTTACCAGGTTGCTTGGGGCCTTGAATAATAATCGGCATCATTATGTACTTCCTCTTCATGCATAGCCATGGGGGGAGGTT[G/A]
TAGATACACATCGTAATGGGCCAAGTGCTATGGCCGCTGCTCATCTCTCCAAAAGGGTTCATGCCATCCGTACTCAAACCAAACCGTATGTTTCGTGCGT
| 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 | 48.00% | 4.00% | 43.57% | 4.44% | NA |
| All Indica | 2759 | 38.20% | 2.10% | 52.77% | 6.96% | NA |
| All Japonica | 1512 | 58.90% | 8.00% | 33.07% | 0.07% | NA |
| Aus | 269 | 72.90% | 0.00% | 22.30% | 4.83% | NA |
| Indica I | 595 | 37.30% | 0.00% | 49.58% | 13.11% | NA |
| Indica II | 465 | 41.30% | 5.20% | 46.88% | 6.67% | NA |
| Indica III | 913 | 34.50% | 1.40% | 61.99% | 2.08% | NA |
| Indica Intermediate | 786 | 41.20% | 2.70% | 47.96% | 8.14% | NA |
| Temperate Japonica | 767 | 95.30% | 0.70% | 3.91% | 0.13% | NA |
| Tropical Japonica | 504 | 7.70% | 18.80% | 73.41% | 0.00% | NA |
| Japonica Intermediate | 241 | 49.80% | 8.70% | 41.49% | 0.00% | NA |
| VI/Aromatic | 96 | 82.30% | 1.00% | 15.62% | 1.04% | NA |
| Intermediate | 90 | 54.40% | 11.10% | 31.11% | 3.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0218320998 | C -> T | LOC_Os02g30740.1 | synonymous_variant ; p.Tyr173Tyr; LOW | synonymous_codon | Average:11.898; most accessible tissue: Minghui63 flag leaf, score: 15.586 | N | N | N | N |
| vg0218320998 | C -> DEL | LOC_Os02g30740.1 | N | frameshift_variant | Average:11.898; most accessible tissue: Minghui63 flag leaf, score: 15.586 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0218320998 | 6.14E-06 | NA | mr1526 | 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 |
| vg0218320998 | NA | 1.13E-06 | mr1623_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 |