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SWEEP filtering results in good polymorphism between genotypes.
After SWEEP filtering with default parameters, a total of 49,876 SNPs was retained.
SWEEP filtering greatly outperformed both methods for percentage of SNPs recovered that are true SNPs relative to homeologous SNPs.
We evaluated SWEEP filtering against Samtools with traditional filtering and GATK (ploidy set to 4×) with traditional filtering.
SWEEP filtering was performed with the following parameters: "-s 1 -d 5 -r 0 –ultimate".
The SWEEP filtering option is simple, allowing three levels of stringency for filtering.
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MEPs will be recorded on a Synergy EMG machine using band-pass filtering 10 Hz–5 kHz, sweep speed 100 m and gain 100 V/div.
Fluorescence signal sampling frequency was 6.67 kHz; when averaged, signal traces represented an average of 2 7 sweeps, and were filtered offline at 300 1000 Hz.
The false-positive rate of traditionally filtered SNPs ranges from 80%to96%6%, whereas the false-positive rate of SWEEP-filtered SNPs ranges from 0.01% to 0.02%.
Because the original detected sweep signal was difficult to distinguish, a time-domain (T-D) gating method for filtering a background signal was introduced.
Parameters of the recording system were as follows: filters: 1 100 Hz, switched off notch filters, sweep time: 250 ms, artifact reject threshold: 50 μV, averaging: 200 sweeps.
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