| Variant ID: vg1119906028 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 19906028 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, C: 0.00, others allele: 0.00, population size: 250. )
AAGGCAGAGGAGGTGGCTAGAGTTGATTAAAGACTATGATCTTAACATTCAATACACACCGGGTAAGGCGAATGTGGTTGCAGATGCTCTAAGCCGTAAG[C/G]
TCGTTCCTCCAACTGTGAGTTGTTTGATAACTGATTTTGAACGGATGGATATCTCCTATTGTTATGTTGGAGTGGCAAGTACCGAGTCACGAGTCATTCT
AGAATGACTCGTGACTCGGTACTTGCCACTCCAACATAACAATAGGAGATATCCATCCGTTCAAAATCAGTTATCAAACAACTCACAGTTGGAGGAACGA[G/C]
CTTACGGCTTAGAGCATCTGCAACCACATTCGCCTTACCCGGTGTGTATTGAATGTTAAGATCATAGTCTTTAATCAACTCTAGCCACCTCCTCTGCCTT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 55.40% | 21.90% | 7.77% | 15.02% | NA |
| All Indica | 2759 | 84.10% | 4.60% | 6.38% | 4.93% | NA |
| All Japonica | 1512 | 5.10% | 53.40% | 3.84% | 37.63% | NA |
| Aus | 269 | 62.80% | 0.40% | 36.80% | 0.00% | NA |
| Indica I | 595 | 96.50% | 1.30% | 2.02% | 0.17% | NA |
| Indica II | 465 | 90.10% | 4.10% | 5.81% | 0.00% | NA |
| Indica III | 913 | 76.20% | 5.30% | 8.11% | 10.41% | NA |
| Indica Intermediate | 786 | 80.20% | 6.70% | 8.02% | 5.09% | NA |
| Temperate Japonica | 767 | 6.50% | 81.00% | 0.65% | 11.86% | NA |
| Tropical Japonica | 504 | 3.60% | 22.00% | 9.13% | 65.28% | NA |
| Japonica Intermediate | 241 | 3.70% | 31.50% | 2.90% | 61.83% | NA |
| VI/Aromatic | 96 | 6.20% | 66.70% | 26.04% | 1.04% | NA |
| Intermediate | 90 | 50.00% | 35.60% | 10.00% | 4.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1119906028 | C -> DEL | LOC_Os11g34050.1 | N | frameshift_variant | Average:7.608; most accessible tissue: Zhenshan97 root, score: 12.891 | N | N | N | N |
| vg1119906028 | C -> G | LOC_Os11g34050.1 | missense_variant ; p.Leu597Val; MODERATE | nonsynonymous_codon ; L597V | Average:7.608; most accessible tissue: Zhenshan97 root, score: 12.891 | unknown | unknown | TOLERATED | 0.37 |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1119906028 | NA | 1.44E-07 | mr1179 | 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 |
| vg1119906028 | NA | 2.83E-10 | mr1549 | 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 |
| vg1119906028 | NA | 4.63E-08 | mr1729 | 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 |
| vg1119906028 | NA | 1.25E-09 | mr1757 | 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 |
| vg1119906028 | NA | 8.10E-09 | mr1864 | 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 |
| vg1119906028 | NA | 4.68E-08 | mr1156_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 |
| vg1119906028 | NA | 6.51E-06 | mr1549_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 |
| vg1119906028 | NA | 4.55E-09 | mr1741_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 |
| vg1119906028 | NA | 2.76E-11 | mr1746_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 |
| vg1119906028 | NA | 2.80E-07 | mr1757_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 |