Search for Variation information by Variation ID:
Detailed information for vg1000647605:
| Variant ID: vg1000647605 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 647605 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CTTGTTCCTGAACAAACGCCTTAGCCATGGTATTATAGGGAAATACCACATCACCTTAGCAGGAATTCTCTTCTTCGTTAGCTGCCCGTCAACCTCACCT[A/G]
GATCATCTCGTCTAATCTTGTATCGTAGTGCTTTACAAACAGGGCATGCTTCTAGGTTCTCGTACTCCTCACCGCGATATAGGATACAATCATTCGGACA
Reverse complement sequence
TGTCCGAATGATTGTATCCTATATCGCGGTGAGGAGTACGAGAACCTAGAAGCATGCCCTGTTTGTAAAGCACTACGATACAAGATTAGACGAGATGATC[T/C]
AGGTGAGGTTGACGGGCAGCTAACGAAGAAGAGAATTCCTGCTAAGGTGATGTGGTATTTCCCTATAATACCATGGCTAAGGCGTTTGTTCAGGAACAAG
Allele Frequencies:
| 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 | 37.30% | 1.30% | 12.25% | 49.15% | NA |
| All Indica | 2759 | 24.70% | 0.00% | 17.22% | 58.06% | NA |
| All Japonica | 1512 | 51.30% | 4.10% | 2.98% | 41.60% | NA |
| Aus | 269 | 73.60% | 0.00% | 13.38% | 13.01% | NA |
| Indica I | 595 | 12.90% | 0.00% | 8.24% | 78.82% | NA |
| Indica II | 465 | 10.50% | 0.00% | 12.47% | 76.99% | NA |
| Indica III | 913 | 41.00% | 0.00% | 26.51% | 32.53% | NA |
| Indica Intermediate | 786 | 23.00% | 0.10% | 16.03% | 60.81% | NA |
| Temperate Japonica | 767 | 80.10% | 7.30% | 0.65% | 11.99% | NA |
| Tropical Japonica | 504 | 8.30% | 0.00% | 5.95% | 85.71% | NA |
| Japonica Intermediate | 241 | 49.80% | 2.50% | 4.15% | 43.57% | NA |
| VI/Aromatic | 96 | 69.80% | 0.00% | 13.54% | 16.67% | NA |
| Intermediate | 90 | 43.30% | 0.00% | 11.11% | 45.56% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1000647605 | A -> G | LOC_Os10g02030.1 | missense_variant ; p.Leu327Pro; MODERATE | nonsynonymous_codon ; L327P | Average:9.309; most accessible tissue: Minghui63 panicle, score: 16.27 | benign  |
0.025 |
TOLERATED | 1.00 |
| vg1000647605 | A -> DEL | LOC_Os10g02030.1 | N | frameshift_variant | Average:9.309; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1000647605 | 5.29E-07 | NA | mr1926 | 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 |
| vg1000647605 | 1.56E-09 | NA | mr1310_2 | 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 |
| vg1000647605 | 4.38E-08 | NA | mr1310_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 |
| vg1000647605 | NA | 2.36E-06 | mr1549_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 |
| vg1000647605 | NA | 4.79E-06 | mr1757_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 |