Search for Variation information by Variation ID:
Detailed information for vg0429172806:
| Variant ID: vg0429172806 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 29172806 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CGTCTGTGGAGACTCTCAGTTGGTTGTTAATCAAGTCATGAAAGAGTGGTCCTGTTTAGATGATAATATGACCGCTTATCGACAAGAGGTACGCAAGTTG[G/A]
AAGATAAATTCGATGGACTTGAGCTCACCCATGTCCTCCGACATAACAATGAGGTAGCCGACAGACTGGCCAATTTTGGTTCAAAACGGGAGGCAGCCCC
Reverse complement sequence
GGGGCTGCCTCCCGTTTTGAACCAAAATTGGCCAGTCTGTCGGCTACCTCATTGTTATGTCGGAGGACATGGGTGAGCTCAAGTCCATCGAATTTATCTT[C/T]
CAACTTGCGTACCTCTTGTCGATAAGCGGTCATATTATCATCTAAACAGGACCACTCTTTCATGACTTGATTAACAACCAACTGAGAGTCTCCACAGACG
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 96.10% | 1.80% | 1.27% | 0.76% | NA |
| All Indica | 2759 | 97.20% | 0.00% | 1.49% | 1.30% | NA |
| All Japonica | 1512 | 93.80% | 5.00% | 1.19% | 0.00% | 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 | 98.70% | 0.00% | 0.86% | 0.43% | NA |
| Indica III | 913 | 93.00% | 0.00% | 3.61% | 3.40% | NA |
| Indica Intermediate | 786 | 99.10% | 0.00% | 0.51% | 0.38% | NA |
| Temperate Japonica | 767 | 90.00% | 8.10% | 1.96% | 0.00% | NA |
| Tropical Japonica | 504 | 99.40% | 0.60% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 94.20% | 4.60% | 1.24% | 0.00% | NA |
| VI/Aromatic | 96 | 89.60% | 10.40% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 0.00% | 1.11% | 0.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0429172806 | G -> DEL | LOC_Os04g48910.1 | N | frameshift_variant | Average:31.338; most accessible tissue: Minghui63 root, score: 40.262 | N | N | N | N |
| vg0429172806 | G -> A | LOC_Os04g48910.1 | missense_variant ; p.Glu523Lys; MODERATE | nonsynonymous_codon ; E523K | Average:31.338; most accessible tissue: Minghui63 root, score: 40.262 | benign  |
0.644 |
TOLERATED | 0.06 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0429172806 | NA | 1.28E-07 | Awn_length | Jap_All | Not | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |
| vg0429172806 | 2.27E-06 | 2.27E-06 | mr1644 | Jap_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 |
| vg0429172806 | NA | 7.44E-08 | mr1038_2 | Jap_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 |
| vg0429172806 | NA | 4.25E-06 | mr1057_2 | Jap_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 |
| vg0429172806 | 1.46E-07 | 1.46E-07 | mr1191_2 | 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 |