| Variant ID: vg1207120422 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 7120422 |
| Reference Allele: A | Alternative Allele: G,C |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GGAGTCGAAGTGCCCCATGGACTCCGCTGCCGCCGGCACCATTATCACCATCTGTTCAGCCGCCACCGCCCATGGCGGCATCATTGTCATCATCCCGTTC[A/G,C]
CCGCCACAGCGGGCAGCAATGCTCCCGCACCCGTGCCGGCGCTGGACGAGGAGGTGAAGGAGGAGAAGTAGTCGCGCAGCGGGGAAGAAGTGCTCGTCGG
CCGACGAGCACTTCTTCCCCGCTGCGCGACTACTTCTCCTCCTTCACCTCCTCGTCCAGCGCCGGCACGGGTGCGGGAGCATTGCTGCCCGCTGTGGCGG[T/C,G]
GAACGGGATGATGACAATGATGCCGCCATGGGCGGTGGCGGCTGAACAGATGGTGATAATGGTGCCGGCGGCAGCGGAGTCCATGGGGCACTTCGACTCC
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 85.60% | 6.20% | 2.56% | 5.46% | C: 0.15% |
| All Indica | 2759 | 99.20% | 0.20% | 0.18% | 0.18% | C: 0.22% |
| All Japonica | 1512 | 57.10% | 18.80% | 7.41% | 16.53% | C: 0.07% |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.30% | 0.20% | 0.17% | 0.34% | NA |
| Indica II | 465 | 98.10% | 0.20% | 0.22% | 0.43% | C: 1.08% |
| Indica III | 913 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.10% | 0.30% | 0.38% | 0.13% | C: 0.13% |
| Temperate Japonica | 767 | 41.90% | 25.00% | 10.82% | 22.29% | NA |
| Tropical Japonica | 504 | 86.70% | 5.60% | 2.18% | 5.56% | NA |
| Japonica Intermediate | 241 | 44.00% | 27.00% | 7.47% | 21.16% | C: 0.41% |
| VI/Aromatic | 96 | 99.00% | 0.00% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 90.00% | 3.30% | 4.44% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1207120422 | A -> C | LOC_Os12g12870.1 | missense_variant ; p.Thr259Pro; MODERATE | nonsynonymous_codon ; T259P | Average:56.305; most accessible tissue: Zhenshan97 flag leaf, score: 80.373 | unknown | unknown | DELETERIOUS | 0.03 |
| vg1207120422 | A -> DEL | LOC_Os12g12870.1 | N | frameshift_variant | Average:56.305; most accessible tissue: Zhenshan97 flag leaf, score: 80.373 | N | N | N | N |
| vg1207120422 | A -> G | LOC_Os12g12870.1 | missense_variant ; p.Thr259Ala; MODERATE | nonsynonymous_codon ; T259A | Average:56.305; most accessible tissue: Zhenshan97 flag leaf, score: 80.373 | unknown | unknown | TOLERATED | 0.57 |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1207120422 | 7.82E-07 | 2.13E-06 | mr1296_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 |
| vg1207120422 | 9.01E-06 | 9.01E-06 | mr1452_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 |
| vg1207120422 | NA | 3.64E-06 | mr1576_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 |
| vg1207120422 | NA | 2.58E-06 | mr1821_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 |