| Variant ID: vg0809652916 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 9652916 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.61, T: 0.39, others allele: 0.00, population size: 66. )
CATATTGAACACGTACCGAAGTGACGGAAAGACCGGCTGCTTGGTTGAAACTTTTCGCAGGCGTCTACGAAGGCACGAAACACGCGAGCGAAGAGGAAGG[T/C]
GAGCCATCGCGAACGAACAGGGAGCAGTCGCGCGAAGCGCTTCCCAAAAACCTTATTGCCGCCTTCTCCCGGTGCAGGACGTCGAAGGCAGAGGTTCCGG
CCGGAACCTCTGCCTTCGACGTCCTGCACCGGGAGAAGGCGGCAATAAGGTTTTTGGGAAGCGCTTCGCGCGACTGCTCCCTGTTCGTTCGCGATGGCTC[A/G]
CCTTCCTCTTCGCTCGCGTGTTTCGTGCCTTCGTAGACGCCTGCGAAAAGTTTCAACCAAGCAGCCGGTCTTTCCGTCACTTCGGTACGTGTTCAATATG
| 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 | 74.40% | 13.10% | 0.13% | 12.42% | NA |
| All Indica | 2759 | 89.40% | 3.90% | 0.04% | 6.67% | NA |
| All Japonica | 1512 | 47.20% | 32.50% | 0.33% | 19.91% | NA |
| Aus | 269 | 97.40% | 0.40% | 0.00% | 2.23% | NA |
| Indica I | 595 | 87.60% | 12.40% | 0.00% | 0.00% | NA |
| Indica II | 465 | 81.90% | 1.90% | 0.00% | 16.13% | NA |
| Indica III | 913 | 92.20% | 0.20% | 0.00% | 7.56% | NA |
| Indica Intermediate | 786 | 92.00% | 2.80% | 0.13% | 5.09% | NA |
| Temperate Japonica | 767 | 32.60% | 57.40% | 0.00% | 10.04% | NA |
| Tropical Japonica | 504 | 62.10% | 1.00% | 0.79% | 36.11% | NA |
| Japonica Intermediate | 241 | 62.70% | 19.50% | 0.41% | 17.43% | NA |
| VI/Aromatic | 96 | 16.70% | 0.00% | 0.00% | 83.33% | NA |
| Intermediate | 90 | 63.30% | 18.90% | 0.00% | 17.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0809652916 | T -> C | LOC_Os08g15870.1 | missense_variant ; p.His3Arg; MODERATE | nonsynonymous_codon ; H3R | Average:38.333; most accessible tissue: Zhenshan97 flag leaf, score: 60.074 | unknown | unknown | TOLERATED | 1.00 |
| vg0809652916 | T -> DEL | LOC_Os08g15870.1 | N | frameshift_variant | Average:38.333; most accessible tissue: Zhenshan97 flag leaf, score: 60.074 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0809652916 | NA | 4.09E-06 | mr1194_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 |
| vg0809652916 | NA | 7.35E-06 | mr1458_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 |
| vg0809652916 | NA | 1.14E-08 | mr1482_2 | 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 |
| vg0809652916 | NA | 7.42E-08 | mr1482_2 | 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 |
| vg0809652916 | NA | 5.86E-06 | mr1588_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 |