| Variant ID: vg1114902966 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 14902966 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GTCACAGTACACCATGAAGTCCTTGCGAGTATCCGGTAAGATTAAAACTGGCGAGGAAACTGGCTTTTCCTTGAGAGTTTGGAACACCTTCTCGCATTGC[G/A]
GGCTCCACACAAATTTTTCTTCCTTCTTCAGCAACTACGTCATGGGTCTGGCAATTTTGGAGAAATTCTCGATGAATCTTCGGTAGTACCCGGCCAAACC
GGTTTGGCCGGGTACTACCGAAGATTCATCGAGAATTTCTCCAAAATTGCCAGACCCATGACGTAGTTGCTGAAGAAGGAAGAAAAATTTGTGTGGAGCC[C/T]
GCAATGCGAGAAGGTGTTCCAAACTCTCAAGGAAAAGCCAGTTTCCTCGCCAGTTTTAATCTTACCGGATACTCGCAAGGACTTCATGGTGTACTGTGAC
| 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 | 78.60% | 2.70% | 5.48% | 13.20% | NA |
| All Indica | 2759 | 79.40% | 2.00% | 5.91% | 12.72% | NA |
| All Japonica | 1512 | 81.80% | 0.00% | 1.12% | 17.06% | NA |
| Aus | 269 | 46.10% | 26.80% | 24.91% | 2.23% | NA |
| Indica I | 595 | 82.20% | 0.70% | 4.20% | 12.94% | NA |
| Indica II | 465 | 83.00% | 1.70% | 4.95% | 10.32% | NA |
| Indica III | 913 | 76.80% | 3.00% | 7.34% | 12.92% | NA |
| Indica Intermediate | 786 | 78.20% | 1.90% | 6.11% | 13.74% | NA |
| Temperate Japonica | 767 | 71.20% | 0.00% | 1.30% | 27.51% | NA |
| Tropical Japonica | 504 | 98.20% | 0.00% | 0.79% | 0.99% | NA |
| Japonica Intermediate | 241 | 81.30% | 0.00% | 1.24% | 17.43% | NA |
| VI/Aromatic | 96 | 95.80% | 1.00% | 2.08% | 1.04% | NA |
| Intermediate | 90 | 80.00% | 0.00% | 11.11% | 8.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1114902966 | G -> A | LOC_Os11g26050.1 | missense_variant&splice_region_variant ; p.Pro777Leu; MODERATE | nonsynonymous_codon ; P777L | Average:11.986; most accessible tissue: Callus, score: 34.082 | unknown | unknown | DELETERIOUS | 0.00 |
| vg1114902966 | G -> DEL | LOC_Os11g26050.1 | N | frameshift_variant | Average:11.986; most accessible tissue: Callus, score: 34.082 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1114902966 | NA | 9.75E-06 | mr1285 | Ind_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 |
| vg1114902966 | NA | 8.61E-09 | mr1855 | Ind_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 |
| vg1114902966 | 3.29E-06 | 2.94E-07 | mr1818_2 | Ind_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 |
| vg1114902966 | NA | 3.63E-07 | mr1855_2 | Ind_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 |
| vg1114902966 | NA | 1.74E-06 | mr1927_2 | Ind_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 |