| Variant ID: vg0713887346 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 13887346 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
ACAGGTTCAGTATCAGCAAGGAGGATCAGCTCAGCCTCAGTTTGCTCCTCAGTACAATCAATTTGAGCCTATACCTCAACAAGCACAAGGGGTGCCTCAG[C/T]
AGAGACCTTGGGCCGATATGTTTGCAGATGTGATGAGAGAGCAGTTTGGGCTTAAGCCAAAGGATACTCGAAACTTGTATCGGCATCCGTACCCTGAGTG
CACTCAGGGTACGGATGCCGATACAAGTTTCGAGTATCCTTTGGCTTAAGCCCAAACTGCTCTCTCATCACATCTGCAAACATATCGGCCCAAGGTCTCT[G/A]
CTGAGGCACCCCTTGTGCTTGTTGAGGTATAGGCTCAAATTGATTGTACTGAGGAGCAAACTGAGGCTGAGCTGATCCTCCTTGCTGATACTGAACCTGT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 74.50% | 6.30% | 5.16% | 14.07% | NA |
| All Indica | 2759 | 69.10% | 6.60% | 6.67% | 17.69% | NA |
| All Japonica | 1512 | 84.70% | 4.80% | 2.58% | 7.94% | NA |
| Aus | 269 | 62.10% | 11.90% | 6.32% | 19.70% | NA |
| Indica I | 595 | 76.10% | 9.60% | 4.87% | 9.41% | NA |
| Indica II | 465 | 71.20% | 5.20% | 6.02% | 17.63% | NA |
| Indica III | 913 | 64.20% | 1.50% | 9.64% | 24.64% | NA |
| Indica Intermediate | 786 | 68.20% | 10.90% | 4.96% | 15.90% | NA |
| Temperate Japonica | 767 | 85.50% | 8.70% | 2.61% | 3.13% | NA |
| Tropical Japonica | 504 | 93.50% | 0.20% | 1.79% | 4.56% | NA |
| Japonica Intermediate | 241 | 63.50% | 2.10% | 4.15% | 30.29% | NA |
| VI/Aromatic | 96 | 94.80% | 5.20% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 84.40% | 6.70% | 4.44% | 4.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0713887346 | C -> DEL | LOC_Os07g24390.1 | N | frameshift_variant | Average:53.923; most accessible tissue: Zhenshan97 young leaf, score: 83.412 | N | N | N | N |
| vg0713887346 | C -> T | LOC_Os07g24390.1 | N | stop_gained | Average:53.923; most accessible tissue: Zhenshan97 young leaf, score: 83.412 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0713887346 | NA | 5.41E-06 | mr1062 | Jap_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 |
| vg0713887346 | NA | 6.52E-07 | mr1210 | Jap_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 |
| vg0713887346 | NA | 4.17E-06 | mr1305 | Jap_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 |
| vg0713887346 | 5.94E-06 | 5.94E-06 | mr1409 | Jap_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 |
| vg0713887346 | NA | 7.15E-07 | mr1585 | Jap_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 |
| vg0713887346 | NA | 9.73E-06 | mr1586 | Jap_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 |
| vg0713887346 | 2.87E-06 | 2.87E-06 | mr1649 | 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 |
| vg0713887346 | NA | 1.09E-06 | mr1585_2 | Jap_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 |