| Variant ID: vg0710881106 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 10881106 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
ATAGAGCTCCTAAAAGAGTTTTGAGATTGCTTCGCTTGGGAGTATTATGAGATGCCCGGACTCAGCCGATCGATTGTTGAACATCGGCTACCTATCAAGC[A/C]
AGGGGGTTAGACCACGCCAGCAACCTCCGAGGAGATGTAAAGCCGATATGCTCGAACCTGTTAAAGCTGAGATCAAACGATTGTATGATGCTGGTTTTAT
ATAAAACCAGCATCATACAATCGTTTGATCTCAGCTTTAACAGGTTCGAGCATATCGGCTTTACATCTCCTCGGAGGTTGCTGGCGTGGTCTAACCCCCT[T/G]
GCTTGATAGGTAGCCGATGTTCAACAATCGATCGGCTGAGTCCGGGCATCTCATAATACTCCCAAGCGAAGCAATCTCAAAACTCTTTTAGGAGCTCTAT
| 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 | 93.90% | 0.30% | 0.40% | 5.40% | NA |
| All Indica | 2759 | 99.10% | 0.00% | 0.11% | 0.76% | NA |
| All Japonica | 1512 | 85.10% | 0.00% | 0.73% | 14.22% | NA |
| Aus | 269 | 93.70% | 4.50% | 0.37% | 1.49% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.90% | 0.00% | 0.00% | 0.11% | NA |
| Indica Intermediate | 786 | 97.10% | 0.00% | 0.38% | 2.54% | NA |
| Temperate Japonica | 767 | 78.20% | 0.00% | 0.91% | 20.86% | NA |
| Tropical Japonica | 504 | 92.90% | 0.00% | 0.40% | 6.75% | NA |
| Japonica Intermediate | 241 | 90.50% | 0.00% | 0.83% | 8.71% | NA |
| VI/Aromatic | 96 | 83.30% | 0.00% | 3.12% | 13.54% | NA |
| Intermediate | 90 | 93.30% | 3.30% | 1.11% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0710881106 | A -> DEL | LOC_Os07g18360.1 | N | frameshift_variant | Average:48.07; most accessible tissue: Minghui63 young leaf, score: 71.254 | N | N | N | N |
| vg0710881106 | A -> C | LOC_Os07g18360.1 | missense_variant ; p.Lys731Gln; MODERATE | nonsynonymous_codon ; K731Q | Average:48.07; most accessible tissue: Minghui63 young leaf, score: 71.254 | unknown | unknown | TOLERATED | 0.47 |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0710881106 | 3.37E-08 | 3.37E-08 | mr1750 | 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 |
| vg0710881106 | 1.08E-06 | 1.08E-06 | mr1987 | 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 |