Setting | Description |
|---|---|
Function | |
Coding Variants • Synonymous • Missense • Nonsense • No-stop • Indels | • By default, show substitutions of all types in the report. Clear the options for the substitution types that are not to be displayed in the report. • By default, show insertions and/or deletions. Clear this option if indels are not to be displayed in the report. |
Non-coding Variants • Splicing Sites Intron [2] Exon [0] | • Select this option to show all variants in splicing site regions, and then specify the intron and exon values to define the splicing site region. |
• All other substitutions | • Selected by default. Show all substitutions that are located outside coding regions. |
• All other indels | • Selected by default. Show all indels that are located outside coding regions. |
Zygosity | |
• Homozygous | • Selected by default. Show homozygous variants in the report. |
• Heterozygous | • Selected by default. Show heterozygous variants in the report. |
Limit Regions – Select this option to show only those variants that occur in a designated region of the reference file. | |
• Gene | • Selected by default. Show the variants that occur only in gene regions. “x” number of bases on either end of the gene region can be shown as well. |
• Exon | • Show the variants that occur only in mRNA regions. “x” number of bases on either end of the mRNA region can be shown as well. |
• CDS | • Show variants that occur only in the coding exons. “x” number of bases on either end of the coding exon region can be shown as well. |
Source | |
• Called by software | • Selected by default. Include all variants that NextGENe automatically identified. |
• Added manually | • Selected by default. Include all variants that you manually added using the Add Mutation function in the Alignment viewer. |
• Confirmed | • Selected by default. Include all variants that you manually confirmed using the Confirm Mutation function in the Alignment viewer. |
• Deleted | • Include all variants that NextGENe automatically deleted and all variants that you deleted using the Delete Mutation function in the Alignment viewer. |
• Negative | • Include the locations of reported SNPs (annotated in the reference file) where the sample data does not include the variant. |
Note: For the source options listed above, see Alignment viewer functions. | |
Reference Database | |
dbSNP | • Reported – Selected by default. Show reported variations as annotated in the reference based on dbSNP. • Unreported – Selected by default. Show unreported variations as annotated in the reference based on dbSNP. |