Search for Variation information by Variation ID:
Detailed information for vg0807399752:
| Variant ID: vg0807399752 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 7399752 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TGCCACGTATTACGGTGCCATCGAGGACATATGGGAACTTGACTATGGTCCTCTCAAGGTTCCTCTGTTCCGGTGCCAATGGGTTAGGTTGACTGATGGA[G/A]
GCGTAATGATTGATGACAGTGGGATGACAACTGTTGACCTTAACAAGGTTGGATACTCGGATGAACCTTTTGTCCTTGCCAATGATGTAACGCAAGTAAC
Reverse complement sequence
GTTACTTGCGTTACATCATTGGCAAGGACAAAAGGTTCATCCGAGTATCCAACCTTGTTAAGGTCAACAGTTGTCATCCCACTGTCATCAATCATTACGC[C/T]
TCCATCAGTCAACCTAACCCATTGGCACCGGAACAGAGGAACCTTGAGAGGACCATAGTCAAGTTCCCATATGTCCTCGATGGCACCGTAATACGTGGCA
Allele Frequencies:
| 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 | 35.20% | 0.10% | 4.44% | 60.18% | NA |
| All Indica | 2759 | 15.20% | 0.30% | 4.86% | 79.70% | NA |
| All Japonica | 1512 | 78.80% | 0.00% | 3.44% | 17.79% | NA |
| Aus | 269 | 3.70% | 0.00% | 5.95% | 90.33% | NA |
| Indica I | 595 | 35.00% | 0.50% | 3.70% | 60.84% | NA |
| Indica II | 465 | 17.00% | 0.00% | 7.31% | 75.70% | NA |
| Indica III | 913 | 1.90% | 0.20% | 3.29% | 94.63% | NA |
| Indica Intermediate | 786 | 14.60% | 0.30% | 6.11% | 79.01% | NA |
| Temperate Japonica | 767 | 62.80% | 0.00% | 5.22% | 31.94% | NA |
| Tropical Japonica | 504 | 96.20% | 0.00% | 2.18% | 1.59% | NA |
| Japonica Intermediate | 241 | 92.90% | 0.00% | 0.41% | 6.64% | NA |
| VI/Aromatic | 96 | 5.20% | 0.00% | 4.17% | 90.62% | NA |
| Intermediate | 90 | 44.40% | 0.00% | 4.44% | 51.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0807399752 | G -> A | LOC_Os08g12500.1 | missense_variant ; p.Gly932Ser; MODERATE | nonsynonymous_codon ; G932S | Average:5.692; most accessible tissue: Minghui63 flower, score: 10.335 | possibly damaging  |
1.893 |
DELETERIOUS | 0.02 |
| vg0807399752 | G -> DEL | LOC_Os08g12500.1 | N | frameshift_variant | Average:5.692; most accessible tissue: Minghui63 flower, score: 10.335 | N | N | N | N |