| Variant ID: vg1109241491 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 9241491 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CACAATCATTTCCTATTTAATTTTACCTATTTTTTTAATAACCGTGTCCAACTCTAAAAATGCTTATATTCTAGTACTGAGGGAGTACATAATCCTATGG[A/C]
TGTCACTAAAATATTTCGACAGCTTTCCAAAATTCTCATATGTATCCAATTCAATTGTTGCACACTTAGTAGGCAGCTGTAAGCCCCCGGCATGGTGTTG
CAACACCATGCCGGGGGCTTACAGCTGCCTACTAAGTGTGCAACAATTGAATTGGATACATATGAGAATTTTGGAAAGCTGTCGAAATATTTTAGTGACA[T/G]
CCATAGGATTATGTACTCCCTCAGTACTAGAATATAAGCATTTTTAGAGTTGGACACGGTTATTAAAAAAATAGGTAAAATTAAATAGGAAATGATTGTG
| 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 | 73.90% | 21.60% | 1.95% | 2.54% | NA |
| All Indica | 2759 | 93.40% | 2.50% | 0.33% | 3.73% | NA |
| All Japonica | 1512 | 48.70% | 45.20% | 5.09% | 0.93% | NA |
| Aus | 269 | 10.40% | 89.20% | 0.37% | 0.00% | NA |
| Indica I | 595 | 95.10% | 0.30% | 0.17% | 4.37% | NA |
| Indica II | 465 | 90.10% | 1.10% | 0.65% | 8.17% | NA |
| Indica III | 913 | 96.80% | 3.10% | 0.00% | 0.11% | NA |
| Indica Intermediate | 786 | 90.20% | 4.30% | 0.64% | 4.83% | NA |
| Temperate Japonica | 767 | 29.50% | 61.70% | 7.17% | 1.69% | NA |
| Tropical Japonica | 504 | 82.90% | 14.50% | 2.38% | 0.20% | NA |
| Japonica Intermediate | 241 | 38.60% | 57.30% | 4.15% | 0.00% | NA |
| VI/Aromatic | 96 | 87.50% | 8.30% | 2.08% | 2.08% | NA |
| Intermediate | 90 | 74.40% | 21.10% | 3.33% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1109241491 | A -> DEL | LOC_Os11g16670.1 | N | frameshift_variant | Average:51.701; most accessible tissue: Zhenshan97 young leaf, score: 65.28 | N | N | N | N |
| vg1109241491 | A -> C | LOC_Os11g16670.1 | missense_variant ; p.Ile199Ser; MODERATE | nonsynonymous_codon ; I199S | Average:51.701; most accessible tissue: Zhenshan97 young leaf, score: 65.28 | unknown | unknown | TOLERATED | 1.00 |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1109241491 | 8.05E-06 | 9.55E-09 | mr1026 | 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 |
| vg1109241491 | NA | 1.08E-06 | mr1161 | 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 |
| vg1109241491 | NA | 7.57E-07 | mr1443 | 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 |
| vg1109241491 | NA | 1.12E-06 | mr1555 | 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 |
| vg1109241491 | NA | 4.69E-09 | mr1364_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 |