| Variant ID: vg1207346320 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 7346320 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
ATTCGTCTACCGAGTATAGAGAGGGGGTCACAGAATTTGTCACATTTGCGGATAATGACAGAAAAAGTAGGATGAGCATGCACATGTTGTGTCCATGTAG[A/G]
GACTGTAAGAATGAACAGATGATCGAACATAGCGATGAAGTGCATGCTCATTTGATAATGAATGGATTCATGAAGAAATGTACCTGCTGGACCAAGCATG
CATGCTTGGTCCAGCAGGTACATTTCTTCATGAATCCATTCATTATCAAATGAGCATGCACTTCATCGCTATGTTCGATCATCTGTTCATTCTTACAGTC[T/C]
CTACATGGACACAACATGTGCATGCTCATCCTACTTTTTCTGTCATTATCCGCAAATGTGACAAATTCTGTGACCCCCTCTCTATACTCGGTAGACGAAT
| 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 | 86.00% | 7.70% | 4.78% | 1.54% | NA |
| All Indica | 2759 | 93.80% | 0.60% | 2.90% | 2.65% | NA |
| All Japonica | 1512 | 68.70% | 22.00% | 9.33% | 0.00% | NA |
| Aus | 269 | 99.60% | 0.00% | 0.37% | 0.00% | NA |
| Indica I | 595 | 96.00% | 0.20% | 2.69% | 1.18% | NA |
| Indica II | 465 | 95.50% | 0.40% | 3.01% | 1.08% | NA |
| Indica III | 913 | 90.50% | 0.80% | 3.83% | 4.93% | NA |
| Indica Intermediate | 786 | 95.20% | 0.90% | 1.91% | 2.04% | NA |
| Temperate Japonica | 767 | 54.40% | 31.80% | 13.82% | 0.00% | NA |
| Tropical Japonica | 504 | 90.30% | 6.20% | 3.57% | 0.00% | NA |
| Japonica Intermediate | 241 | 68.90% | 24.10% | 7.05% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 83.30% | 12.20% | 4.44% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1207346320 | A -> DEL | LOC_Os12g13180.1 | N | frameshift_variant | Average:37.63; most accessible tissue: Minghui63 flag leaf, score: 50.629 | N | N | N | N |
| vg1207346320 | A -> G | LOC_Os12g13180.1 | synonymous_variant ; p.Arg138Arg; LOW | synonymous_codon | Average:37.63; most accessible tissue: Minghui63 flag leaf, score: 50.629 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1207346320 | NA | 7.84E-11 | Heading_date | All | Not | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |
| vg1207346320 | NA | 3.24E-07 | mr1364 | 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 |
| vg1207346320 | NA | 8.14E-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 |
| vg1207346320 | NA | 7.42E-08 | mr1576_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 |
| vg1207346320 | 1.13E-06 | 5.85E-08 | mr1648_2 | 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 |