| Variant ID: vg0900072657 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 72657 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
CTGCGTGTAGGGCCGCACGCCTTCTCCGCTCTTCAAGATAGTCGAGGTCGTCGCGGCGAAGATCATCCTGGTTGGCCTCATCGTACAGCGTGACGCGAGG[C/G]
GAGCCCAGGGAAAGCTCCGAAGGTAGGACCGCCTCGGCGCCATACACCAGGAAAAAGGGTGTTTCCCCTGTGGCGCGACTTGGAGTGGTCCGAATCGCCC
GGGCGATTCGGACCACTCCAAGTCGCGCCACAGGGGAAACACCCTTTTTCCTGGTGTATGGCGCCGAGGCGGTCCTACCTTCGGAGCTTTCCCTGGGCTC[G/C]
CCTCGCGTCACGCTGTACGATGAGGCCAACCAGGATGATCTTCGCCGCGACGACCTCGACTATCTTGAAGAGCGGAGAAGGCGTGCGGCCCTACACGCAG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 48.10% | 0.30% | 2.75% | 48.90% | NA |
| All Indica | 2759 | 28.60% | 0.50% | 3.01% | 67.92% | NA |
| All Japonica | 1512 | 86.90% | 0.10% | 0.60% | 12.43% | NA |
| Aus | 269 | 27.10% | 0.00% | 10.78% | 62.08% | NA |
| Indica I | 595 | 47.40% | 0.00% | 1.18% | 51.43% | NA |
| Indica II | 465 | 28.80% | 0.40% | 3.44% | 67.31% | NA |
| Indica III | 913 | 17.60% | 0.90% | 3.83% | 77.66% | NA |
| Indica Intermediate | 786 | 27.00% | 0.40% | 3.18% | 69.47% | NA |
| Temperate Japonica | 767 | 76.40% | 0.00% | 1.17% | 22.43% | NA |
| Tropical Japonica | 504 | 99.40% | 0.00% | 0.00% | 0.60% | NA |
| Japonica Intermediate | 241 | 94.20% | 0.40% | 0.00% | 5.39% | NA |
| VI/Aromatic | 96 | 33.30% | 0.00% | 7.29% | 59.38% | NA |
| Intermediate | 90 | 70.00% | 0.00% | 2.22% | 27.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0900072657 | C -> G | LOC_Os09g01040.1 | synonymous_variant ; p.Ser650Ser; LOW | synonymous_codon | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0900072657 | C -> DEL | LOC_Os09g01040.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0900072657 | NA | 3.01E-06 | mr1134 | 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 |
| vg0900072657 | NA | 4.93E-06 | mr1504 | 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 |
| vg0900072657 | NA | 3.51E-06 | mr1097_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 |
| vg0900072657 | 9.90E-06 | 7.74E-10 | mr1134_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 |
| vg0900072657 | 5.66E-06 | 5.66E-06 | mr1670_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 |
| vg0900072657 | NA | 5.86E-07 | mr1672_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 |