| Variant ID: vg1214356031 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 14356031 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
CTGTATCGATTACCTCAAAGATGGATATGCAATTGGAGTACCTGTGCCCCGACACGAGGGCAGATTGAGTGGCAAGGGAACGATAGGAAAGAAGAGATTC[A/G]
TCACCCATGATCACAAATCATTCCAAGAAGCTCACTTCAGCGTCCTTCATCAGTTTGCTATCGTTGAGCCTTACATCGAACAACATATCGAACTAATACG
CGTATTAGTTCGATATGTTGTTCGATGTAAGGCTCAACGATAGCAAACTGATGAAGGACGCTGAAGTGAGCTTCTTGGAATGATTTGTGATCATGGGTGA[T/C]
GAATCTCTTCTTTCCTATCGTTCCCTTGCCACTCAATCTGCCCTCGTGTCGGGGCACAGGTACTCCAATTGCATATCCATCTTTGAGGTAATCGATACAG
| 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 | 38.20% | 11.70% | 1.57% | 48.56% | NA |
| All Indica | 2759 | 18.20% | 8.40% | 2.28% | 71.11% | NA |
| All Japonica | 1512 | 77.10% | 19.50% | 0.07% | 3.37% | NA |
| Aus | 269 | 25.70% | 2.60% | 1.86% | 69.89% | NA |
| Indica I | 595 | 28.90% | 6.70% | 1.85% | 62.52% | NA |
| Indica II | 465 | 27.50% | 3.20% | 3.01% | 66.24% | NA |
| Indica III | 913 | 6.40% | 11.00% | 2.63% | 80.07% | NA |
| Indica Intermediate | 786 | 18.30% | 9.80% | 1.78% | 70.10% | NA |
| Temperate Japonica | 767 | 89.00% | 5.70% | 0.13% | 5.08% | NA |
| Tropical Japonica | 504 | 67.30% | 31.90% | 0.00% | 0.79% | NA |
| Japonica Intermediate | 241 | 59.30% | 37.30% | 0.00% | 3.32% | NA |
| VI/Aromatic | 96 | 25.00% | 0.00% | 1.04% | 73.96% | NA |
| Intermediate | 90 | 48.90% | 21.10% | 4.44% | 25.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1214356031 | A -> DEL | LOC_Os12g25000.1 | N | frameshift_variant | Average:25.616; most accessible tissue: Minghui63 flag leaf, score: 59.912 | N | N | N | N |
| vg1214356031 | A -> G | LOC_Os12g25000.1 | missense_variant ; p.Ile640Val; MODERATE | nonsynonymous_codon ; I640V | Average:25.616; most accessible tissue: Minghui63 flag leaf, score: 59.912 | unknown | unknown | TOLERATED | 0.70 |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1214356031 | NA | 6.93E-06 | mr1236 | 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 |
| vg1214356031 | NA | 3.56E-08 | mr1002_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 |
| vg1214356031 | NA | 7.21E-06 | mr1554_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 |
| vg1214356031 | 4.13E-06 | NA | mr1916_2 | 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 |
| vg1214356031 | NA | 2.12E-09 | mr1916_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 |
| vg1214356031 | NA | 8.55E-06 | mr1944_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 |