| Variant ID: vg1202111176 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 2111176 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.51, G: 0.50, others allele: 0.00, population size: 82. )
TGAGTGCGATAAGAGCTTTGAGGAGCTCAAGAAGAAATTAGTATCCGCACCAGTTTTGATTCTGCCCAACCAGATGAAAGACTTCCAAGTCTATTGCGAC[A/G]
CATCCCGCCACGGGCTTGGGTGTGTTCTAATGCAGGAAGGCAGAGTGGTGGCGTATGCCTCACGACAGCTGCGTCCACACGAAGGGAATTATCCAACCCA
TGGGTTGGATAATTCCCTTCGTGTGGACGCAGCTGTCGTGAGGCATACGCCACCACTCTGCCTTCCTGCATTAGAACACACCCAAGCCCGTGGCGGGATG[T/C]
GTCGCAATAGACTTGGAAGTCTTTCATCTGGTTGGGCAGAATCAAAACTGGTGCGGATACTAATTTCTTCTTGAGCTCCTCAAAGCTCTTATCGCACTCA
| 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 | 61.00% | 32.60% | 3.77% | 2.67% | NA |
| All Indica | 2759 | 91.30% | 3.40% | 4.02% | 1.23% | NA |
| All Japonica | 1512 | 4.80% | 86.00% | 3.17% | 6.08% | NA |
| Aus | 269 | 92.90% | 5.60% | 1.49% | 0.00% | NA |
| Indica I | 595 | 88.20% | 3.20% | 5.55% | 3.03% | NA |
| Indica II | 465 | 91.00% | 4.50% | 4.09% | 0.43% | NA |
| Indica III | 913 | 94.60% | 1.60% | 2.63% | 1.10% | NA |
| Indica Intermediate | 786 | 90.10% | 5.00% | 4.45% | 0.51% | NA |
| Temperate Japonica | 767 | 0.80% | 95.40% | 0.13% | 3.65% | NA |
| Tropical Japonica | 504 | 12.50% | 66.30% | 8.93% | 12.30% | NA |
| Japonica Intermediate | 241 | 1.20% | 97.10% | 0.83% | 0.83% | NA |
| VI/Aromatic | 96 | 6.20% | 83.30% | 10.42% | 0.00% | NA |
| Intermediate | 90 | 38.90% | 55.60% | 5.56% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1202111176 | A -> DEL | LOC_Os12g04910.1 | N | frameshift_variant | Average:24.391; most accessible tissue: Minghui63 young leaf, score: 42.042 | N | N | N | N |
| vg1202111176 | A -> G | LOC_Os12g04910.1 | missense_variant ; p.Thr854Ala; MODERATE | nonsynonymous_codon ; T854A | Average:24.391; most accessible tissue: Minghui63 young leaf, score: 42.042 | unknown | unknown | TOLERATED | 1.00 |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1202111176 | NA | 7.89E-06 | mr1508 | 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 |
| vg1202111176 | NA | 7.49E-06 | mr1681 | 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 |
| vg1202111176 | NA | 6.70E-07 | mr1690 | 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 |
| vg1202111176 | NA | 2.54E-28 | mr1238_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 |
| vg1202111176 | NA | 4.81E-26 | mr1484_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 |
| vg1202111176 | NA | 2.90E-07 | mr1804_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 |
| vg1202111176 | NA | 4.86E-33 | mr1841_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 |
| vg1202111176 | NA | 3.83E-20 | mr1900_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 |
| vg1202111176 | NA | 3.86E-19 | mr1945_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 |
| vg1202111176 | 1.34E-06 | 1.34E-06 | mr1973_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 |