Setting | Description |
|---|---|
Basic | |
Coverage | Selected by default. The total number of reads that are aligned at the variant location. |
Alt # | The total number of reads that contain the alternate (variant) nucleotide at the variant position. |
Alt % | The percentage of total reads that contain the alternate (variant) nucleotide at the variant position. |
Overall Score | Selected by default. An empirical estimation of the likelihood that a given variant call is real and not an artifact of sequencing or alignment errors. See Overall Mutation Score. |
Ref #(F,R) | The number of reads that show the reference nucleotide in the forward direction and the number of reads that show the reference nucleotide in the reverse direction. |
Alt #(F,R) | The number of reads that show the alternate (variant) nucleotide in the forward direction and the number of reads that show the alternate (variant) nucleotide in the reverse direction. |
Details | |
A #(F,R), C #(F,R), G #(F,R), T#(F,R) | Selected by default. The number of reads that show the indicated base at the variant location in the forward direction and the number of reads that show the indicated base at the variant location in the reverse direction. |
Del #(F,R) | Selected by default. The number of reads that show a deletion at the variant location in the forward direction and the number of reads that show a deletion at the variant location in the reverse direction. |
Ins #(F,R) | Selected by default. The number of reads that show an insertion at the variant location in the forward direction and the number of reads that show an insertion in the reverse direction at the variant location. |
A(%), C(%), G(%), T(%) | The percentage of reads that show the indicated base at the variant location. |
Del(%) | The percentage of reads that show a deletion at the variant location. |
Ins(%) | The percentage of reads that show an insertion at the variant location. |
A Score, C Score, G Score, T Score | Essentially an allele balance score for each individual allele. It is scaled to be similar to the Overall Mutation score, but it does not contribute to the overall score. • If the allele F/R ratio is > 3 x the F/R ratio for all the reads at the indicated position, or is < 1/3 x the F/R ratio for all the reads at the indicated position, then the score for the allele is zero. • If the position has no calls that correspond to the indicated allele, then the score for the allele is again zero. • Otherwise, the score is calculated based on the F/R ratio for the allele and the F/R ratio for all the reads at the indicated position. The closer that these two values are, then higher the allele score. The maximum allele score for any allele is 27. |
Del Score | For deletion alleles. See the description for A Score, C Score, G Score, T Score. |
Ins Score | For insertion alleles. See the description for A Score, C Score, G Score, T Score. |
Allele Score | For the alternate allele. See the description for A Score, C Score, G Score, T Score. |
Ambiguous Gain Penalty | Display the Ambiguous Gain penalty value for the variant. See Ambiguous Gain penalty/Ambiguous Loss penalty. |
Ambiguous Loss Penalty | Display the Ambiguous Loss penalty value for the variant. See Ambiguous Gain penalty/Ambiguous Loss penalty. |
Balance ratio relative to counts | Show the smaller of the two ratios: • #F/#R–The ratio of the number (count) of forward reads with the variant to the number of reverse reads with the variant. • #R/#F–The ratio of the number (count) of reverse reads with the variant to the number of forward reads with the variant. |
Balance ratio relative to percentage | Show the smaller of the two ratios: • %ALTF/%ALTR–The ratio of the percentage of forward reads with the alternate allele to the percentage of reverse reads with the alternate allele. • %ALTR/%ALTF–The ratio of the percentage of reverse reads with the alternate allele to the percentage of forward reads with the alternate allele Note: This value is useful for regions that have overall directionally-biased coverage. |
Note: You can set the filters based on the balance ratios on the Filter tab, Bias sub-tab. See Filter tab, Bias sub-tab. | |
Other | |
Check Allele Counts for Negative Mutations | When negative variants are included in the report, calculate and display the allele frequencies for these positions. |
Calculate statistics based on original reads for Condensation/Elongation projects | Editable only if the loaded project used Condensation or Elongation. When selected, display statistics based on the original reads. |