| Variant ID: vg1202795096 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 2795096 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CATGAAAACATAAAGGAATGGTGCGATGCAAGGTACTCACAGCACGAGCGAAGTCCTGGTTGCGGTGCCTGGCATAGAGGTCTCTAGTGCTCGCAACGTG[G/A]
GGCTGCTGCTCCAAGGGAGCGAAGGTGACCCTAGTACGGGTACGTGGCTGGTACCAGCGTAGGTAGGCCTGGTACGACTCCTCAGTGTGTGGCTCTCCCT
AGGGAGAGCCACACACTGAGGAGTCGTACCAGGCCTACCTACGCTGGTACCAGCCACGTACCCGTACTAGGGTCACCTTCGCTCCCTTGGAGCAGCAGCC[C/T]
CACGTTGCGAGCACTAGAGACCTCTATGCCAGGCACCGCAACCAGGACTTCGCTCGTGCTGTGAGTACCTTGCATCGCACCATTCCTTTATGTTTTCATG
| 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 | 95.10% | 2.00% | 1.23% | 1.69% | NA |
| All Indica | 2759 | 95.30% | 3.10% | 1.34% | 0.29% | NA |
| All Japonica | 1512 | 99.00% | 0.70% | 0.13% | 0.20% | NA |
| Aus | 269 | 68.00% | 0.00% | 6.69% | 25.28% | NA |
| Indica I | 595 | 87.60% | 8.10% | 4.37% | 0.00% | NA |
| Indica II | 465 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica III | 913 | 98.50% | 0.90% | 0.44% | 0.22% | NA |
| Indica Intermediate | 786 | 94.90% | 3.40% | 0.89% | 0.76% | NA |
| Temperate Japonica | 767 | 99.70% | 0.00% | 0.26% | 0.00% | NA |
| Tropical Japonica | 504 | 98.20% | 1.20% | 0.00% | 0.60% | NA |
| Japonica Intermediate | 241 | 98.30% | 1.70% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 97.80% | 0.00% | 1.11% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1202795096 | G -> DEL | LOC_Os12g06040.1 | N | frameshift_variant | Average:54.406; most accessible tissue: Minghui63 flag leaf, score: 75.341 | N | N | N | N |
| vg1202795096 | G -> A | LOC_Os12g06040.1 | synonymous_variant ; p.Pro1321Pro; LOW | synonymous_codon | Average:54.406; most accessible tissue: Minghui63 flag leaf, score: 75.341 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1202795096 | NA | 2.80E-08 | mr1070 | 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 |
| vg1202795096 | NA | 2.81E-08 | mr1128 | 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 |
| vg1202795096 | NA | 1.62E-06 | mr1692 | 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 |
| vg1202795096 | NA | 4.58E-08 | mr1740 | 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 |
| vg1202795096 | NA | 1.72E-07 | mr1128_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 |