Variant ID: vg0712599200 (JBrowse) | Variation Type: SNP |
Chromosome: chr07 | Position: 12599200 |
Reference Allele: C | Alternative Allele: G |
Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
CGTAGCTCAATCTTTCTCCAGTCAGGGAGATCAAAACAACCCCAGCTCCAGTGCCTGAAAGCCTCTTCGACCCATCAAAATGCATGGTCCAATACTCCAT[C/G]
TTCTCCTCGGGCATGTCTTCTTGGCACTCGGTCCACTTGGCGACAAAGTCGGCTAAAGCTTGGGACTTAATCGAAGTTCGTGGCTTGAAGGATATATCCA
TGGATATATCCTTCAAGCCACGAACTTCGATTAAGTCCCAAGCTTTAGCCGACTTTGTCGCCAAGTGGACCGAGTGCCAAGAAGACATGCCCGAGGAGAA[G/C]
ATGGAGTATTGGACCATGCATTTTGATGGGTCGAAGAGGCTTTCAGGCACTGGAGCTGGGGTTGTTTTGATCTCCCTGACTGGAGAAAGATTGAGCTACG
Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 96.60% | 0.30% | 0.23% | 2.90% | NA |
All Indica | 2759 | 99.90% | 0.00% | 0.00% | 0.07% | NA |
All Japonica | 1512 | 89.70% | 0.70% | 0.66% | 8.93% | NA |
Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | 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 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 99.70% | 0.00% | 0.00% | 0.25% | NA |
Temperate Japonica | 767 | 80.30% | 1.00% | 1.17% | 17.47% | NA |
Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 98.80% | 0.40% | 0.41% | 0.41% | NA |
VI/Aromatic | 96 | 96.90% | 3.10% | 0.00% | 0.00% | NA |
Intermediate | 90 | 97.80% | 1.10% | 1.11% | 0.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0712599200 | C -> DEL | LOC_Os07g22420.1 | N | frameshift_variant | Average:52.591; most accessible tissue: Minghui63 flag leaf, score: 82.521 | N | N | N | N |
vg0712599200 | C -> G | LOC_Os07g22420.1 | missense_variant ; p.Lys1100Asn; MODERATE | nonsynonymous_codon ; K1100N | Average:52.591; most accessible tissue: Minghui63 flag leaf, score: 82.521 | benign | 0.776 | TOLERATED | 0.07 |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0712599200 | 2.78E-06 | 2.78E-06 | mr1067 | 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 |