Variant ID: vg1004721834 (JBrowse) | Variation Type: SNP |
Chromosome: chr10 | Position: 4721834 |
Reference Allele: G | Alternative Allele: C |
Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
GCTCCGTACGAAGCACTGTATGGTCGGAAGTGCCGCACTCCGCTTTTGTGGGATCAAACGGGAGAACGTCAGGTTTTCGGGAAGCAGAAGAGAAGGTAAA[G/C]
ATCATTCAAGAAAGGTTGCGTGTGGCTCAGTCTCGCCATAAGAGTTATGCCGACAATCGCCGCAGAGATTTGAGTTTTGAAGAAGGAGATTATGTGTACC
GGTACACATAATCTCCTTCTTCAAAACTCAAATCTCTGCGGCGATTGTCGGCATAACTCTTATGGCGAGACTGAGCCACACGCAACCTTTCTTGAATGAT[C/G]
TTTACCTTCTCTTCTGCTTCCCGAAAACCTGACGTTCTCCCGTTTGATCCCACAAAAGCGGAGTGCGGCACTTCCGACCATACAGTGCTTCGTACGGAGC
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 | 86.60% | 2.30% | 1.54% | 9.54% | NA |
All Indica | 2759 | 91.70% | 0.30% | 1.41% | 6.63% | NA |
All Japonica | 1512 | 87.80% | 6.50% | 0.20% | 5.49% | NA |
Aus | 269 | 23.80% | 0.00% | 11.15% | 65.06% | NA |
Indica I | 595 | 80.30% | 0.00% | 0.50% | 19.16% | NA |
Indica II | 465 | 94.40% | 0.00% | 0.43% | 5.16% | NA |
Indica III | 913 | 95.50% | 0.90% | 2.19% | 1.42% | NA |
Indica Intermediate | 786 | 94.10% | 0.00% | 1.78% | 4.07% | NA |
Temperate Japonica | 767 | 95.20% | 0.10% | 0.00% | 4.69% | NA |
Tropical Japonica | 504 | 79.80% | 19.00% | 0.00% | 1.19% | NA |
Japonica Intermediate | 241 | 80.90% | 0.80% | 1.24% | 17.01% | NA |
VI/Aromatic | 96 | 95.80% | 0.00% | 1.04% | 3.12% | NA |
Intermediate | 90 | 88.90% | 3.30% | 0.00% | 7.78% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg1004721834 | G -> C | LOC_Os10g08702.1 | missense_variant ; p.Lys1101Asn; MODERATE | nonsynonymous_codon ; K1101N | Average:12.562; most accessible tissue: Minghui63 young leaf, score: 32.638 | possibly damaging | 1.918 | DELETERIOUS | 0.00 |
vg1004721834 | G -> DEL | LOC_Os10g08702.1 | N | frameshift_variant | Average:12.562; most accessible tissue: Minghui63 young leaf, score: 32.638 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg1004721834 | 2.83E-06 | NA | mr1817 | 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 |