| Variant ID: vg0713133131 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 13133131 |
| Reference Allele: C | Alternative Allele: A,T |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, A: 0.02, others allele: 0.00, population size: 99. )
CGACGCCTCCGACCCAAGAAGATGTGCGTGGGGGGCCGGATGCCCGCCTCAATATTGAGCGCCGACGCAATGGTCGTCGTGCTGCCCACGCAACGGAGTG[C/A,T]
GCTTCCTCGTCCGGAGCGCCACTTCAGTCTGGGCATGGGGGCCAGCCTCCCATGTCCCCGGTTGGCGGTGCCGGCTGTCGAGCCTTTGTGGCGAGCCTTC
GAAGGCTCGCCACAAAGGCTCGACAGCCGGCACCGCCAACCGGGGACATGGGAGGCTGGCCCCCATGCCCAGACTGAAGTGGCGCTCCGGACGAGGAAGC[G/T,A]
CACTCCGTTGCGTGGGCAGCACGACGACCATTGCGTCGGCGCTCAATATTGAGGCGGGCATCCGGCCCCCCACGCACATCTTCTTGGGTCGGAGGCGTCG
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 49.70% | 42.20% | 1.06% | 7.09% | NA |
| All Indica | 2759 | 81.50% | 15.10% | 0.91% | 2.50% | NA |
| All Japonica | 1512 | 1.50% | 80.40% | 1.19% | 16.93% | NA |
| Aus | 269 | 18.20% | 81.80% | 0.00% | 0.00% | NA |
| Indica I | 595 | 97.30% | 2.50% | 0.17% | 0.00% | NA |
| Indica II | 465 | 86.70% | 11.20% | 1.08% | 1.08% | NA |
| Indica III | 913 | 72.40% | 21.90% | 0.55% | 5.15% | NA |
| Indica Intermediate | 786 | 77.00% | 19.10% | 1.78% | 2.16% | NA |
| Temperate Japonica | 767 | 2.00% | 68.80% | 1.56% | 27.64% | NA |
| Tropical Japonica | 504 | 0.60% | 96.00% | 0.40% | 2.98% | NA |
| Japonica Intermediate | 241 | 1.70% | 84.60% | 1.66% | 12.03% | NA |
| VI/Aromatic | 96 | 2.10% | 92.70% | 2.08% | 3.12% | NA |
| Intermediate | 90 | 28.90% | 57.80% | 5.56% | 7.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0713133131 | C -> DEL | N | N | silent_mutation | Average:58.629; most accessible tissue: Zhenshan97 flag leaf, score: 78.761 | N | N | N | N |
| vg0713133131 | C -> A | LOC_Os07g23300.1 | intron_variant ; MODIFIER | silent_mutation | Average:58.629; most accessible tissue: Zhenshan97 flag leaf, score: 78.761 | N | N | N | N |
| vg0713133131 | C -> T | LOC_Os07g23300.1 | intron_variant ; MODIFIER | N | Average:58.629; most accessible tissue: Zhenshan97 flag leaf, score: 78.761 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0713133131 | NA | 7.46E-06 | mr1872 | 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 |
| vg0713133131 | 5.04E-06 | 9.90E-07 | mr1039_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 |
| vg0713133131 | NA | 4.12E-06 | mr1558_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 |
| vg0713133131 | 1.95E-06 | 9.69E-08 | mr1632_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 |