| Variant ID: vg0432263043 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 32263043 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GCCTACGAGATCATCGCCCGCACCTGGACCTCGATTTTCTCCGTGAGGGTTTTGCTCATTCTCGGAGGACTCCGGCGGAGATAGACCACCTGGCGAGGTC[G/A]
ATGGCGCCGTTGGCGGAGAAGATCTTCCAGTCTATGGACTGGCGTTGGCCTTCTTGGTAGTCTTCGTACCCTGTGATAGATATCTCAGGAAAAAGGTGTA
TACACCTTTTTCCTGAGATATCTATCACAGGGTACGAAGACTACCAAGAAGGCCAACGCCAGTCCATAGACTGGAAGATCTTCTCCGCCAACGGCGCCAT[C/T]
GACCTCGCCAGGTGGTCTATCTCCGCCGGAGTCCTCCGAGAATGAGCAAAACCCTCACGGAGAAAATCGAGGTCCAGGTGCGGGCGATGATCTCGTAGGC
| 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 | 92.10% | 6.60% | 1.27% | 0.02% | NA |
| All Indica | 2759 | 99.50% | 0.30% | 0.18% | 0.00% | NA |
| All Japonica | 1512 | 77.20% | 19.40% | 3.24% | 0.07% | NA |
| Aus | 269 | 97.40% | 0.40% | 2.23% | 0.00% | NA |
| Indica I | 595 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica II | 465 | 98.50% | 1.50% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.30% | 0.10% | 0.55% | 0.00% | NA |
| Indica Intermediate | 786 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 77.70% | 18.00% | 4.17% | 0.13% | NA |
| Tropical Japonica | 504 | 73.80% | 23.60% | 2.58% | 0.00% | NA |
| Japonica Intermediate | 241 | 83.00% | 15.40% | 1.66% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 92.20% | 7.80% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0432263043 | G -> DEL | LOC_Os04g54150.1 | N | frameshift_variant | Average:46.537; most accessible tissue: Minghui63 young leaf, score: 62.741 | N | N | N | N |
| vg0432263043 | G -> A | LOC_Os04g54150.1 | synonymous_variant ; p.Ser761Ser; LOW | synonymous_codon | Average:46.537; most accessible tissue: Minghui63 young leaf, score: 62.741 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0432263043 | 6.66E-06 | NA | mr1205 | 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 |
| vg0432263043 | NA | 5.26E-06 | mr1830 | 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 |
| vg0432263043 | NA | 2.44E-06 | mr1960 | 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 |
| vg0432263043 | 1.84E-06 | 1.84E-06 | mr1333_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 |