| Variant ID: vg0908388909 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 8388909 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CTTGTCGTTCAGACAAGAGCCACGAGCCGACGAGAATAACTTCCGAAGCGACAAGGTCCTGGTGTCCTATCCACAAAACCAGGAAACACACTTTGCAAGC[T/C]
TGCTGGGTTTTTCTCAACGTCCGCGCCGAAATTCGCGCCTGCAAAGAGAGTGGAATTCAGCGTATTTCTCCAACCCGTGATGTCTATTGTCCTATTCACA
TGTGAATAGGACAATAGACATCACGGGTTGGAGAAATACGCTGAATTCCACTCTCTTTGCAGGCGCGAATTTCGGCGCGGACGTTGAGAAAAACCCAGCA[A/G]
GCTTGCAAAGTGTGTTTCCTGGTTTTGTGGATAGGACACCAGGACCTTGTCGCTTCGGAAGTTATTCTCGTCGGCTCGTGGCTCTTGTCTGAACGACAAG
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 76.50% | 10.60% | 3.22% | 9.63% | NA |
| All Indica | 2759 | 77.50% | 14.80% | 3.55% | 4.24% | NA |
| All Japonica | 1512 | 73.80% | 4.20% | 2.71% | 19.31% | NA |
| Aus | 269 | 78.80% | 9.70% | 2.97% | 8.55% | NA |
| Indica I | 595 | 84.20% | 3.70% | 4.87% | 7.23% | NA |
| Indica II | 465 | 96.10% | 2.60% | 1.08% | 0.22% | NA |
| Indica III | 913 | 60.20% | 32.20% | 3.94% | 3.61% | NA |
| Indica Intermediate | 786 | 81.30% | 10.10% | 3.56% | 5.09% | NA |
| Temperate Japonica | 767 | 95.80% | 0.30% | 1.30% | 2.61% | NA |
| Tropical Japonica | 504 | 46.60% | 10.70% | 3.17% | 39.48% | NA |
| Japonica Intermediate | 241 | 60.60% | 2.90% | 6.22% | 30.29% | NA |
| VI/Aromatic | 96 | 74.00% | 3.10% | 4.17% | 18.75% | NA |
| Intermediate | 90 | 88.90% | 4.40% | 1.11% | 5.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0908388909 | T -> DEL | LOC_Os09g14180.1 | N | frameshift_variant | Average:36.152; most accessible tissue: Minghui63 flag leaf, score: 77.494 | N | N | N | N |
| vg0908388909 | T -> C | LOC_Os09g14180.1 | synonymous_variant ; p.Ala164Ala; LOW | synonymous_codon | Average:36.152; most accessible tissue: Minghui63 flag leaf, score: 77.494 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0908388909 | 2.40E-06 | 2.40E-06 | mr1513 | 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 |
| vg0908388909 | NA | 6.67E-06 | mr1695 | 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 |
| vg0908388909 | NA | 9.91E-06 | mr1964 | 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 |