Variant ID: vg0714479069 (JBrowse) | Variation Type: INDEL |
Chromosome: chr07 | Position: 14479069 |
Reference Allele: A | Alternative Allele: G,AGAG |
Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
AGGACCACGATCTCGAGGTTCACTATCACCCTGGCAAGGCAAACGTCGTGGCCGACGCTTTGAGTCGTAAGAGCCATTGCAATCATCTGAGAATGGAAGG[A/G,AGAG]
ATGGCTCCTGAGCTTAAAGAGGAATATGCCCAGCTAAACCTACATATAGTGCCTCGTGGACGGATAAACACCCTTGACATTCAACCTCTTTTGAGAACCC
GGGTTCTCAAAAGAGGTTGAATGTCAAGGGTGTTTATCCGTCCACGAGGCACTATATGTAGGTTTAGCTGGGCATATTCCTCTTTAAGCTCAGGAGCCAT[T/C,CTCT]
CCTTCCATTCTCAGATGATTGCAATGGCTCTTACGACTCAAAGCGTCGGCCACGACGTTTGCCTTGCCAGGGTGATAGTGAACCTCGAGATCGTGGTCCT
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 | 41.60% | 32.40% | 7.34% | 18.71% | NA |
All Indica | 2759 | 24.10% | 47.10% | 9.46% | 19.35% | NA |
All Japonica | 1512 | 75.20% | 5.00% | 3.44% | 16.34% | NA |
Aus | 269 | 28.30% | 41.30% | 8.18% | 22.30% | NA |
Indica I | 595 | 26.20% | 61.00% | 2.52% | 10.25% | NA |
Indica II | 465 | 28.60% | 44.10% | 12.90% | 14.41% | NA |
Indica III | 913 | 18.70% | 40.00% | 10.95% | 30.34% | NA |
Indica Intermediate | 786 | 26.00% | 46.70% | 10.94% | 16.41% | NA |
Temperate Japonica | 767 | 77.70% | 6.10% | 2.48% | 13.69% | NA |
Tropical Japonica | 504 | 79.80% | 3.00% | 1.59% | 15.67% | NA |
Japonica Intermediate | 241 | 57.70% | 5.80% | 10.37% | 26.14% | NA |
VI/Aromatic | 96 | 43.80% | 19.80% | 8.33% | 28.12% | NA |
Intermediate | 90 | 50.00% | 27.80% | 4.44% | 17.78% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0714479069 | A -> DEL | LOC_Os07g25340.1 | N | frameshift_variant | Average:17.905; most accessible tissue: Callus, score: 40.135 | N | N | N | N |
vg0714479069 | A -> AGAG | LOC_Os07g25340.1 | inframe_insertion ; p.Gly889_Met890insGlu; MODERATE | N | Average:17.905; most accessible tissue: Callus, score: 40.135 | N | N | N | N |
vg0714479069 | A -> G | LOC_Os07g25340.1 | synonymous_variant ; p.Gly889Gly; LOW | synonymous_codon | Average:17.905; most accessible tissue: Callus, score: 40.135 | N | N | N | N |
vg0714479069 | A -> G | LOC_Os07g25340.1 | synonymous_variant ; p.Gly889Gly; LOW | nonsynonymous_codon ; G889R | Average:17.905; most accessible tissue: Callus, score: 40.135 | probably damaging | 2.199 | TOLERATED | 0.10 |
vg0714479069 | A -> G | LOC_Os07g25340.1 | synonymous_variant ; p.Gly889Gly; LOW | nonsynonymous_codon ; G889E | Average:17.905; most accessible tissue: Callus, score: 40.135 | benign | 0.626 | TOLERATED | 0.18 |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0714479069 | 2.19E-06 | 2.62E-07 | mr1428 | 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 |