Search for Variation information by Variation ID:
Detailed information for vg0319757475:
| Variant ID: vg0319757475 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 19757475 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TAGTGAGCCAAACGATAGAACTCGTGCAGGTACTTTGTGACGGTCAAATCTGCTTGCTTCAGATAGCGAAACTCTCGTTTTCTTAATGTGATCATTCCTG[C/T]
GGGAACATGTGATCTCCTGAATACAGATGAAAACTCGTTCCAGGTGATGGTATGTCCTTCTGGCTGTGATGCTTCGTAGCTATCCCACCACTCTGAAGCC
Reverse complement sequence
GGCTTCAGAGTGGTGGGATAGCTACGAAGCATCACAGCCAGAAGGACATACCATCACCTGGAACGAGTTTTCATCTGTATTCAGGAGATCACATGTTCCC[G/A]
CAGGAATGATCACATTAAGAAAACGAGAGTTTCGCTATCTGAAGCAAGCAGATTTGACCGTCACAAAGTACCTGCACGAGTTCTATCGTTTGGCTCACTA
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 33.70% | 0.60% | 3.81% | 61.83% | NA |
| All Indica | 2759 | 6.10% | 1.10% | 4.57% | 88.29% | NA |
| All Japonica | 1512 | 83.80% | 0.00% | 3.17% | 13.03% | NA |
| Aus | 269 | 13.00% | 0.00% | 0.37% | 86.62% | NA |
| Indica I | 595 | 4.50% | 0.00% | 2.35% | 93.11% | NA |
| Indica II | 465 | 5.20% | 1.10% | 3.66% | 90.11% | NA |
| Indica III | 913 | 6.00% | 2.20% | 6.79% | 84.99% | NA |
| Indica Intermediate | 786 | 7.90% | 0.50% | 4.20% | 87.40% | NA |
| Temperate Japonica | 767 | 94.80% | 0.00% | 0.52% | 4.69% | NA |
| Tropical Japonica | 504 | 66.30% | 0.00% | 6.55% | 27.18% | NA |
| Japonica Intermediate | 241 | 85.50% | 0.00% | 4.56% | 9.96% | NA |
| VI/Aromatic | 96 | 78.10% | 0.00% | 1.04% | 20.83% | NA |
| Intermediate | 90 | 55.60% | 0.00% | 4.44% | 40.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0319757475 | C -> T | LOC_Os03g35670.1 | missense_variant ; p.Ala517Thr; MODERATE | nonsynonymous_codon ; A517T | Average:6.461; most accessible tissue: Minghui63 flower, score: 10.335 | benign  |
0.38 |
TOLERATED | 0.23 |
| vg0319757475 | C -> DEL | LOC_Os03g35670.1 | N | frameshift_variant | Average:6.461; most accessible tissue: Minghui63 flower, score: 10.335 | N | N | N | N |