| Variant ID: vg0401768023 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 1768023 |
| Reference Allele: G | Alternative Allele: C |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 90. )
CCCTTGACCACGACGTCGAGCTTCAACTCCTGCATCACGCGCCGTAGGTCGCGCACATGGCGCTCGTCGATGTCGTCGCCGAAGCAGAAGCGCACGGCCA[G/C]
CGGGAACAAGGCGTCGTGGACGACGTCGCGGACGCCCACCTCGCCGCCGTCGGCACCACGGGCGGCGATGTCGGCGACGAGGGCGTCGACGGCCTTCTGC
GCAGAAGGCCGTCGACGCCCTCGTCGCCGACATCGCCGCCCGTGGTGCCGACGGCGGCGAGGTGGGCGTCCGCGACGTCGTCCACGACGCCTTGTTCCCG[C/G]
TGGCCGTGCGCTTCTGCTTCGGCGACGACATCGACGAGCGCCATGTGCGCGACCTACGGCGCGTGATGCAGGAGTTGAAGCTCGACGTCGTGGTCAAGGG
| 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 | 53.10% | 16.50% | 2.03% | 28.33% | NA |
| All Indica | 2759 | 31.10% | 19.50% | 3.04% | 46.39% | NA |
| All Japonica | 1512 | 97.20% | 1.70% | 0.00% | 1.19% | NA |
| Aus | 269 | 33.50% | 58.40% | 2.60% | 5.58% | NA |
| Indica I | 595 | 15.60% | 3.00% | 2.52% | 78.82% | NA |
| Indica II | 465 | 40.00% | 24.70% | 3.66% | 31.61% | NA |
| Indica III | 913 | 38.30% | 28.70% | 3.18% | 29.79% | NA |
| Indica Intermediate | 786 | 29.10% | 18.10% | 2.93% | 49.87% | NA |
| Temperate Japonica | 767 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 93.10% | 4.00% | 0.00% | 2.98% | NA |
| Japonica Intermediate | 241 | 97.10% | 1.70% | 0.00% | 1.24% | NA |
| VI/Aromatic | 96 | 53.10% | 44.80% | 0.00% | 2.08% | NA |
| Intermediate | 90 | 47.80% | 20.00% | 5.56% | 26.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0401768023 | G -> C | LOC_Os04g03870.1 | missense_variant ; p.Leu143Val; MODERATE | nonsynonymous_codon ; L143V | Average:67.744; most accessible tissue: Minghui63 panicle, score: 85.556 | unknown | unknown | TOLERATED | 0.42 |
| vg0401768023 | G -> DEL | LOC_Os04g03870.1 | N | frameshift_variant | Average:67.744; most accessible tissue: Minghui63 panicle, score: 85.556 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0401768023 | 7.93E-07 | NA | mr1472_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 |
| vg0401768023 | 1.67E-06 | NA | mr1472_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 |
| vg0401768023 | 1.09E-06 | 1.09E-06 | mr1666_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 |
| vg0401768023 | NA | 6.36E-06 | mr1761_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 |