Search for Variation information by Variation ID:
Detailed information for vg0319757555:
| Variant ID: vg0319757555 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 19757555 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TCTTAATGTGATCATTCCTGCGGGAACATGTGATCTCCTGAATACAGATGAAAACTCGTTCCAGGTGATGGTATGTCCTTCTGGCTGTGATGCTTCGTAG[C/T]
TATCCCACCACTCTGAAGCCGGTCCAACCAGCTGAGGAGTTGCGAAGCCAACCCGCTCCTGGTCGGTGCACTGAATCAACCCTAGCTTCTTCTCGATTGT
Reverse complement sequence
ACAATCGAGAAGAAGCTAGGGTTGATTCAGTGCACCGACCAGGAGCGGGTTGGCTTCGCAACTCCTCAGCTGGTTGGACCGGCTTCAGAGTGGTGGGATA[G/A]
CTACGAAGCATCACAGCCAGAAGGACATACCATCACCTGGAACGAGTTTTCATCTGTATTCAGGAGATCACATGTTCCCGCAGGAATGATCACATTAAGA
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 | 34.70% | 0.10% | 15.40% | 49.75% | NA |
| All Indica | 2759 | 7.20% | 0.20% | 21.53% | 71.04% | NA |
| All Japonica | 1512 | 85.00% | 0.00% | 4.83% | 10.19% | NA |
| Aus | 269 | 12.60% | 0.00% | 13.01% | 74.35% | NA |
| Indica I | 595 | 4.00% | 0.00% | 12.94% | 83.03% | NA |
| Indica II | 465 | 7.50% | 0.00% | 18.92% | 73.55% | NA |
| Indica III | 913 | 9.10% | 0.30% | 28.04% | 62.54% | NA |
| Indica Intermediate | 786 | 7.40% | 0.30% | 22.01% | 70.36% | NA |
| Temperate Japonica | 767 | 95.70% | 0.00% | 3.39% | 0.91% | NA |
| Tropical Japonica | 504 | 67.70% | 0.00% | 6.94% | 25.40% | NA |
| Japonica Intermediate | 241 | 87.10% | 0.00% | 4.98% | 7.88% | NA |
| VI/Aromatic | 96 | 75.00% | 1.00% | 7.29% | 16.67% | NA |
| Intermediate | 90 | 55.60% | 0.00% | 21.11% | 23.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0319757555 | C -> T | LOC_Os03g35670.1 | missense_variant ; p.Ser490Asn; MODERATE | nonsynonymous_codon ; S490N | Average:6.461; most accessible tissue: Minghui63 flower, score: 10.335 | benign  |
0.069 |
TOLERATED | 1.00 |
| vg0319757555 | C -> DEL | LOC_Os03g35670.1 | N | frameshift_variant | Average:6.461; most accessible tissue: Minghui63 flower, score: 10.335 | N | N | N | N |