| Variant ID: vg1000628000 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 628000 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.81, T: 0.19, others allele: 0.00, population size: 89. )
CAGCAAGAAATCGACGATGACCCATGTACACAATCTTCCTACAGTGTTTAAGATCCGTACTTTCTGTTTCATCCATACAGTGAGTGCAAGCCTTGTACCC[T/C]
TTGTTGGACTGCCCGGATAGGTTGCTAAGTGCAGGCCAATCGTTGATGGTTACGAACAGCAGCGCTAGTAGGTTAAATTCCTCCTGTTTGTCTTCGTCCC
GGGACGAAGACAAACAGGAGGAATTTAACCTACTAGCGCTGCTGTTCGTAACCATCAACGATTGGCCTGCACTTAGCAACCTATCCGGGCAGTCCAACAA[A/G]
GGGTACAAGGCTTGCACTCACTGTATGGATGAAACAGAAAGTACGGATCTTAAACACTGTAGGAAGATTGTGTACATGGGTCATCGTCGATTTCTTGCTG
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 27.00% | 19.30% | 48.37% | 5.35% | NA |
| All Indica | 2759 | 12.00% | 32.00% | 54.58% | 1.49% | NA |
| All Japonica | 1512 | 55.80% | 0.70% | 30.16% | 13.36% | NA |
| Aus | 269 | 8.20% | 3.00% | 86.62% | 2.23% | NA |
| Indica I | 595 | 4.20% | 45.50% | 47.06% | 3.19% | NA |
| Indica II | 465 | 27.10% | 11.80% | 59.78% | 1.29% | NA |
| Indica III | 913 | 6.70% | 38.00% | 54.98% | 0.33% | NA |
| Indica Intermediate | 786 | 15.00% | 26.60% | 56.74% | 1.65% | NA |
| Temperate Japonica | 767 | 82.50% | 0.30% | 11.47% | 5.74% | NA |
| Tropical Japonica | 504 | 17.50% | 1.40% | 55.16% | 25.99% | NA |
| Japonica Intermediate | 241 | 50.60% | 0.80% | 37.34% | 11.20% | NA |
| VI/Aromatic | 96 | 45.80% | 2.10% | 52.08% | 0.00% | NA |
| Intermediate | 90 | 42.20% | 7.80% | 45.56% | 4.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1000628000 | T -> C | LOC_Os10g01984.1 | synonymous_variant ; p.Lys431Lys; LOW | synonymous_codon | Average:20.505; most accessible tissue: Minghui63 young leaf, score: 26.082 | N | N | N | N |
| vg1000628000 | T -> DEL | LOC_Os10g01984.1 | N | frameshift_variant | Average:20.505; most accessible tissue: Minghui63 young leaf, score: 26.082 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1000628000 | NA | 9.87E-06 | mr1300 | 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 |
| vg1000628000 | NA | 2.77E-07 | mr1310 | 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 |
| vg1000628000 | NA | 9.85E-06 | mr1482 | 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 |
| vg1000628000 | NA | 2.03E-08 | mr1926 | 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 |
| vg1000628000 | NA | 2.78E-07 | mr1310_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 |
| vg1000628000 | NA | 4.18E-09 | mr1563_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 |
| vg1000628000 | NA | 1.40E-06 | mr1780_2 | 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 |