Variant ID: vg1210160121 (JBrowse) | Variation Type: SNP |
Chromosome: chr12 | Position: 10160121 |
Reference Allele: A | Alternative Allele: G |
Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
GAGTTGCGACATGGCCCAAACTCGCGAGATGGCGTCTGCCCGAGAGGATATCCGACTGGCTGCAGCCACGGCAAGCGAAGGAGAAGTGCCCGCTACCAAG[A/G]
TTTCAAAGAGCGGAGAAAGCGAAGCCAAGACTAAGAAGATTCCCCTAGATCCCTCTGATCCTACTAAAACTGCTGTAATAGGCGCCGAGTTAGATTGTAA
TTACAATCTAACTCGGCGCCTATTACAGCAGTTTTAGTAGGATCAGAGGGATCTAGGGGAATCTTCTTAGTCTTGGCTTCGCTTTCTCCGCTCTTTGAAA[T/C]
CTTGGTAGCGGGCACTTCTCCTTCGCTTGCCGTGGCTGCAGCCAGTCGGATATCCTCTCGGGCAGACGCCATCTCGCGAGTTTGGGCCATGTCGCAACTC
Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 39.60% | 0.70% | 4.80% | 54.82% | NA |
All Indica | 2759 | 13.00% | 1.20% | 5.94% | 79.85% | NA |
All Japonica | 1512 | 78.60% | 0.00% | 2.25% | 19.18% | NA |
Aus | 269 | 76.60% | 0.70% | 5.20% | 17.47% | NA |
Indica I | 595 | 9.40% | 0.00% | 5.21% | 85.38% | NA |
Indica II | 465 | 17.20% | 4.10% | 5.16% | 73.55% | NA |
Indica III | 913 | 6.80% | 0.30% | 6.90% | 85.98% | NA |
Indica Intermediate | 786 | 20.50% | 1.40% | 5.85% | 72.26% | NA |
Temperate Japonica | 767 | 89.60% | 0.00% | 1.69% | 8.74% | NA |
Tropical Japonica | 504 | 65.30% | 0.00% | 1.79% | 32.94% | NA |
Japonica Intermediate | 241 | 71.40% | 0.00% | 4.98% | 23.65% | NA |
VI/Aromatic | 96 | 69.80% | 0.00% | 13.54% | 16.67% | NA |
Intermediate | 90 | 58.90% | 0.00% | 2.22% | 38.89% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg1210160121 | A -> DEL | LOC_Os12g17740.1 | N | frameshift_variant | Average:23.398; most accessible tissue: Minghui63 flag leaf, score: 58.568 | N | N | N | N |
vg1210160121 | A -> G | LOC_Os12g17740.1 | missense_variant ; p.Ile942Val; MODERATE | nonsynonymous_codon ; I942V | Average:23.398; most accessible tissue: Minghui63 flag leaf, score: 58.568 | benign | 0.053 | TOLERATED | 0.39 |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg1210160121 | 1.49E-06 | 1.49E-06 | mr1926 | 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 |
vg1210160121 | NA | 1.98E-07 | mr1002_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 |