| Variant ID: vg0502034831 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 2034831 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CGGGAGGGGGTGGAAGTAACAACCATAAGGACCGCAAGCGTAAGCCTGAGGAACTTGTTGCAACCACTACTCACTCTTCTCGACAGCGCTCGCTCGTCAA[C/T]
ACGTTCGACAAGATCATGAACTCCCAATGCCCGCATCACCCTAACTCCAACCACGCGGCCAAAGATTGTTTCGTCTACAAGCATTTCGCGGAACAATACA
TGTATTGTTCCGCGAAATGCTTGTAGACGAAACAATCTTTGGCCGCGTGGTTGGAGTTAGGGTGATGCGGGCATTGGGAGTTCATGATCTTGTCGAACGT[G/A]
TTGACGAGCGAGCGCTGTCGAGAAGAGTGAGTAGTGGTTGCAACAAGTTCCTCAGGCTTACGCTTGCGGTCCTTATGGTTGTTACTTCCACCCCCTCCCG
| 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 | 88.70% | 3.30% | 4.36% | 3.68% | NA |
| All Indica | 2759 | 89.90% | 3.90% | 4.57% | 1.70% | NA |
| All Japonica | 1512 | 89.20% | 0.90% | 1.52% | 8.40% | NA |
| Aus | 269 | 81.80% | 8.20% | 10.04% | 0.00% | NA |
| Indica I | 595 | 99.20% | 0.00% | 0.84% | 0.00% | NA |
| Indica II | 465 | 93.50% | 3.40% | 3.01% | 0.00% | NA |
| Indica III | 913 | 81.70% | 6.90% | 7.78% | 3.61% | NA |
| Indica Intermediate | 786 | 90.10% | 3.60% | 4.58% | 1.78% | NA |
| Temperate Japonica | 767 | 98.60% | 0.00% | 0.13% | 1.30% | NA |
| Tropical Japonica | 504 | 76.40% | 2.00% | 2.38% | 19.25% | NA |
| Japonica Intermediate | 241 | 85.90% | 1.70% | 4.15% | 8.30% | NA |
| VI/Aromatic | 96 | 64.60% | 8.30% | 27.08% | 0.00% | NA |
| Intermediate | 90 | 92.20% | 3.30% | 4.44% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0502034831 | C -> T | LOC_Os05g04420.1 | synonymous_variant ; p.Asn651Asn; LOW | synonymous_codon | Average:21.15; most accessible tissue: Zhenshan97 flag leaf, score: 40.929 | N | N | N | N |
| vg0502034831 | C -> DEL | LOC_Os05g04420.1 | N | frameshift_variant | Average:21.15; most accessible tissue: Zhenshan97 flag leaf, score: 40.929 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0502034831 | NA | 5.87E-06 | mr1264_2 | 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 |
| vg0502034831 | 9.64E-06 | 2.78E-07 | mr1878_2 | 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 |
| vg0502034831 | 3.66E-07 | NA | mr1949_2 | 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 |