| Variant ID: vg0809553553 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 9553553 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CAGTTGCTTCAGAGGGTTCTAGGCCAGTATTGCTATTCGACTTGTACCGGCTTGCACCGCATGTTGGACATTCATCTAAAGAAGCGTACTCTTTCTTGTA[C/T]
AGTATGCAGTGATTTACGCACATATGAATCTTTTCCACACCAAGTGAAAGGGGGCATATGAGTTTCTTTGCTTGATATGTGTTGGATGGTAGTGAGTTAG
CTAACTCACTACCATCCAACACATATCAAGCAAAGAAACTCATATGCCCCCTTTCACTTGGTGTGGAAAAGATTCATATGTGCGTAAATCACTGCATACT[G/A]
TACAAGAAAGAGTACGCTTCTTTAGATGAATGTCCAACATGCGGTGCAAGCCGGTACAAGTCGAATAGCAATACTGGCCTAGAACCCTCTGAAGCAACTG
| 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 | 17.00% | 5.00% | 6.58% | 71.46% | NA |
| All Indica | 2759 | 5.00% | 7.80% | 10.04% | 77.13% | NA |
| All Japonica | 1512 | 42.10% | 1.10% | 1.52% | 55.29% | NA |
| Aus | 269 | 2.20% | 0.00% | 1.12% | 96.65% | NA |
| Indica I | 595 | 13.30% | 1.00% | 1.18% | 84.54% | NA |
| Indica II | 465 | 3.00% | 15.30% | 18.06% | 63.66% | NA |
| Indica III | 913 | 0.30% | 9.40% | 10.30% | 79.96% | NA |
| Indica Intermediate | 786 | 5.30% | 6.70% | 11.70% | 76.21% | NA |
| Temperate Japonica | 767 | 73.10% | 0.30% | 0.00% | 26.60% | NA |
| Tropical Japonica | 504 | 2.20% | 3.00% | 4.56% | 90.28% | NA |
| Japonica Intermediate | 241 | 26.60% | 0.00% | 0.00% | 73.44% | NA |
| VI/Aromatic | 96 | 1.00% | 0.00% | 2.08% | 96.88% | NA |
| Intermediate | 90 | 23.30% | 3.30% | 6.67% | 66.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0809553553 | C -> T | LOC_Os08g15760.1 | synonymous_variant ; p.Leu128Leu; LOW | synonymous_codon | Average:8.695; most accessible tissue: Minghui63 young leaf, score: 13.864 | N | N | N | N |
| vg0809553553 | C -> DEL | LOC_Os08g15760.1 | N | frameshift_variant | Average:8.695; most accessible tissue: Minghui63 young leaf, score: 13.864 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0809553553 | NA | 2.66E-12 | mr1069 | 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 |
| vg0809553553 | 4.83E-06 | 7.70E-06 | mr1069 | 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 |
| vg0809553553 | NA | 9.69E-06 | mr1224 | 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 |
| vg0809553553 | NA | 6.45E-06 | mr1404 | 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 |
| vg0809553553 | NA | 2.85E-07 | mr1780 | 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 |
| vg0809553553 | NA | 3.51E-06 | mr1918 | Ind_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 |