| Variant ID: vg0720056770 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 20056770 |
| Reference Allele: G | Alternative Allele: C |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CTGGCGAAGCCAACATGTTTCCGCCACGGCGTTGGCCACGGCTCGGTACTCTGCTTCGGCGCTGGAACGGGAGACTGTGTTCTGTCGCTTGTCGCTTGGA[G/C]
GACCAAGAAATCAGGTTGGCACCAAGAAACACGGCATAGCCCGAGGTGGACTTCCTCGTGTCGGGACAACCGGCCCAATCAGCATCAGAATAAGCAACCA
TGGTTGCTTATTCTGATGCTGATTGGGCCGGTTGTCCCGACACGAGGAAGTCCACCTCGGGCTATGCCGTGTTTCTTGGTGCCAACCTGATTTCTTGGTC[C/G]
TCCAAGCGACAAGCGACAGAACACAGTCTCCCGTTCCAGCGCCGAAGCAGAGTACCGAGCCGTGGCCAACGCCGTGGCGGAAACATGTTGGCTTCGCCAG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 57.70% | 11.60% | 1.40% | 29.33% | NA |
| All Indica | 2759 | 28.90% | 19.70% | 2.39% | 49.00% | NA |
| All Japonica | 1512 | 99.30% | 0.20% | 0.00% | 0.46% | NA |
| Aus | 269 | 96.70% | 0.40% | 0.00% | 2.97% | NA |
| Indica I | 595 | 12.80% | 39.30% | 1.51% | 46.39% | NA |
| Indica II | 465 | 25.80% | 21.10% | 4.09% | 49.03% | NA |
| Indica III | 913 | 35.80% | 8.30% | 2.41% | 53.45% | NA |
| Indica Intermediate | 786 | 35.00% | 17.20% | 2.04% | 45.80% | NA |
| Temperate Japonica | 767 | 99.00% | 0.30% | 0.00% | 0.78% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.40% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 76.70% | 2.20% | 0.00% | 21.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0720056770 | G -> DEL | LOC_Os07g33570.1 | N | frameshift_variant | Average:36.4; most accessible tissue: Zhenshan97 root, score: 65.566 | N | N | N | N |
| vg0720056770 | G -> C | LOC_Os07g33570.1 | synonymous_variant ; p.Ser804Ser; LOW | synonymous_codon | Average:36.4; most accessible tissue: Zhenshan97 root, score: 65.566 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0720056770 | NA | 9.18E-06 | mr1114 | 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 |
| vg0720056770 | NA | 3.96E-08 | mr1486 | 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 |
| vg0720056770 | NA | 1.43E-07 | mr1486_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 |