| Variant ID: vg0907578649 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 7578649 |
| Reference Allele: C | Alternative Allele: A,T |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TTGACGGGTTTGCAAGGGGCGAGGAGGATTCCAAGCGACGGCAAGCTATACAAGCTGAGTACGACAAAGCCTCCGTCGCCGCTGCTGAAGCTCAAGCACA[C/A,T]
GTTCAAGTTGCCGAACCACCTCCCCTCTTCGTTCGCTAGTCTCAGCCGGCGATCCAAGGACAGCCGCCATGGCAAAGCCAAGCTCCCATAACTTGGAGAA
TTCTCCAAGTTATGGGAGCTTGGCTTTGCCATGGCGGCTGTCCTTGGATCGCCGGCTGAGACTAGCGAACGAAGAGGGGAGGTGGTTCGGCAACTTGAAC[G/T,A]
TGTGCTTGAGCTTCAGCAGCGGCGACGGAGGCTTTGTCGTACTCAGCTTGTATAGCTTGCCGTCGCTTGGAATCCTCCTCGCCCCTTGCAAACCCGTCAA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 48.00% | 7.50% | 28.27% | 16.14% | T: 0.04% |
| All Indica | 2759 | 31.60% | 2.00% | 43.71% | 22.69% | NA |
| All Japonica | 1512 | 72.10% | 19.20% | 3.97% | 4.56% | T: 0.13% |
| Aus | 269 | 56.90% | 0.40% | 21.93% | 20.82% | NA |
| Indica I | 595 | 49.20% | 1.80% | 31.26% | 17.65% | NA |
| Indica II | 465 | 35.90% | 1.50% | 36.99% | 25.59% | NA |
| Indica III | 913 | 12.80% | 1.30% | 60.13% | 25.74% | NA |
| Indica Intermediate | 786 | 37.50% | 3.20% | 38.04% | 21.25% | NA |
| Temperate Japonica | 767 | 78.90% | 6.90% | 5.74% | 8.34% | T: 0.13% |
| Tropical Japonica | 504 | 76.00% | 22.60% | 0.99% | 0.40% | NA |
| Japonica Intermediate | 241 | 42.30% | 51.50% | 4.56% | 1.24% | T: 0.41% |
| VI/Aromatic | 96 | 96.90% | 0.00% | 1.04% | 2.08% | NA |
| Intermediate | 90 | 67.80% | 10.00% | 11.11% | 11.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0907578649 | C -> DEL | LOC_Os09g13150.1 | N | frameshift_variant | Average:9.46; most accessible tissue: Minghui63 root, score: 13.235 | N | N | N | N |
| vg0907578649 | C -> T | LOC_Os09g13150.1 | splice_region_variant&synonymous_variant ; p.His548His; LOW | synonymous_codon | Average:9.46; most accessible tissue: Minghui63 root, score: 13.235 | N | N | N | N |
| vg0907578649 | C -> A | LOC_Os09g13150.1 | missense_variant&splice_region_variant ; p.His548Gln; MODERATE | nonsynonymous_codon ; H548Q | Average:9.46; most accessible tissue: Minghui63 root, score: 13.235 | unknown | unknown | TOLERATED | 1.00 |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0907578649 | 5.71E-08 | 1.19E-06 | mr1263 | 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 |
| vg0907578649 | 5.71E-08 | 1.19E-06 | mr1451 | 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 |