| Variant ID: vg0507093492 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 7093492 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
TTGGAGCAATCACTTCGGCAGCAGTACAGAAGTTTGTATGGAAAAACATTGTTTGCCGTTTTGGAGTGCCAAAAGAGTTCATTACTAACAACGACAAGCA[A/G]
TTTGACTCTGATAAGTTCAGAGAAATGTGCGAAGGGCTTAACCTGGAAATCAGGTTCGCGTCGGTCGCGCACCCGCAGTCAAATGGGGCGGCCAAACGTA
TACGTTTGGCCGCCCCATTTGACTGCGGGTGCGCGACCGACGCGAACCTGATTTCCAGGTTAAGCCCTTCGCACATTTCTCTGAACTTATCAGAGTCAAA[T/C]
TGCTTGTCGTTGTTAGTAATGAACTCTTTTGGCACTCCAAAACGGCAAACAATGTTTTTCCATACAAACTTCTGTACTGCTGCCGAAGTGATTGCTCCAA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 91.00% | 0.20% | 4.15% | 4.63% | NA |
| All Indica | 2759 | 99.60% | 0.10% | 0.11% | 0.11% | NA |
| All Japonica | 1512 | 74.70% | 0.30% | 11.51% | 13.56% | NA |
| Aus | 269 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.10% | 0.20% | 0.00% | 0.65% | NA |
| Indica III | 913 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.50% | 0.10% | 0.38% | 0.00% | NA |
| Temperate Japonica | 767 | 94.50% | 0.00% | 0.52% | 4.95% | NA |
| Tropical Japonica | 504 | 43.10% | 0.80% | 30.36% | 25.79% | NA |
| Japonica Intermediate | 241 | 77.60% | 0.00% | 7.05% | 15.35% | NA |
| VI/Aromatic | 96 | 76.00% | 0.00% | 18.75% | 5.21% | NA |
| Intermediate | 90 | 90.00% | 2.20% | 1.11% | 6.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0507093492 | A -> DEL | LOC_Os05g12340.1 | N | frameshift_variant | Average:34.548; most accessible tissue: Minghui63 panicle, score: 53.77 | N | N | N | N |
| vg0507093492 | A -> G | LOC_Os05g12340.1 | synonymous_variant ; p.Gln928Gln; LOW | synonymous_codon | Average:34.548; most accessible tissue: Minghui63 panicle, score: 53.77 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0507093492 | NA | 8.70E-06 | mr1083 | 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 |
| vg0507093492 | 8.19E-07 | 8.18E-07 | mr1131 | 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 |
| vg0507093492 | NA | 6.81E-06 | mr1072_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 |