Search for Variation information by Variation ID:
Detailed information for vg1008612253:
| Variant ID: vg1008612253 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 8612253 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CTTTCAGCCCCAGCAAAGAATTGTCGTCGATGGAAGAAGTTGTGTCTCTCCCCGACCTACTCCAGGCCAAGCAAAGGGCGATACCAAGCAGAAGACCGTC[A/C]
TCCGCTTCAACCAGCAATCAGAAGGAAGCTTCTCCTGTGAATGATAGCAATATGCAGTCCTATCACATCATCACAGAACCAATCAAGGATAATGCAGTCA
Reverse complement sequence
TGACTGCATTATCCTTGATTGGTTCTGTGATGATGTGATAGGACTGCATATTGCTATCATTCACAGGAGAAGCTTCCTTCTGATTGCTGGTTGAAGCGGA[T/G]
GACGGTCTTCTGCTTGGTATCGCCCTTTGCTTGGCCTGGAGTAGGTCGGGGAGAGACACAACTTCTTCCATCGACGACAATTCTTTGCTGGGGCTGAAAG
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 14.70% | 0.00% | 4.78% | 80.47% | NA |
| All Indica | 2759 | 1.10% | 0.00% | 5.22% | 93.73% | NA |
| All Japonica | 1512 | 42.70% | 0.10% | 3.57% | 53.70% | NA |
| Aus | 269 | 0.00% | 0.00% | 0.00% | 100.00% | NA |
| Indica I | 595 | 0.80% | 0.00% | 0.50% | 98.66% | NA |
| Indica II | 465 | 1.10% | 0.00% | 0.43% | 98.49% | NA |
| Indica III | 913 | 0.80% | 0.00% | 12.16% | 87.08% | NA |
| Indica Intermediate | 786 | 1.50% | 0.00% | 3.56% | 94.91% | NA |
| Temperate Japonica | 767 | 59.30% | 0.00% | 1.30% | 39.37% | NA |
| Tropical Japonica | 504 | 8.70% | 0.00% | 8.33% | 82.94% | NA |
| Japonica Intermediate | 241 | 60.60% | 0.40% | 0.83% | 38.17% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 19.79% | 80.21% | NA |
| Intermediate | 90 | 24.40% | 0.00% | 10.00% | 65.56% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1008612253 | A -> C | LOC_Os10g17150.1 | missense_variant ; p.Ile404Leu; MODERATE | nonsynonymous_codon ; I404L | Average:4.409; most accessible tissue: Minghui63 panicle, score: 7.125 | benign  |
0.572 |
TOLERATED | 0.05 |
| vg1008612253 | A -> DEL | LOC_Os10g17150.1 | N | frameshift_variant | Average:4.409; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |