Sentence examples for base calls with a from inspiring English sources

First, raw sequence data were cleaned up with QCleaner software (Amelieff): low-quality reads (>20% of the base calls with a Phred score <20) were discarded; reads shorter than 32 and reads containing five or more N were also discarded; base calls at both ends with a Phred score <20 were trimmed.

Sequence ends were trimmed until the first and last 10 bases contained fewer than 5 base calls with a confidence score (phred score) lower than 30.

For variant calling using CRISP, reads with low mapping quality (<20) and base calls with a low quality score (<10) were discarded.

This means that the script filtered out all variant positions that did not have at least 2 genotypes, each with 2 different base calls with a minimum phred score of 20 and within good quality context (5 bases on each side with a minimum phred score of 15).

Bowtie2 options are used where alignment scores are set to be equal to the number of base matches minus three times the number of base mismatches (down-weighted if they are lower quality base calls), with a gap open penalty of 2 and a gap extension penalty of 3. A staged alignment procedure is employed to accelerate read mapping and alignment.

We also filtered out base calls with a quality value below 17, i.e. base calls with an error probability >0.02.

Consensus sequences were considered as valid when at least 98% of the nts were base-called with a PHRAP score above 40.

Sequences not meeting our production quality criteria (at least 100 bases called with a quality over 20) were discarded.

After alignment, sequence variants were called based on quantitative thresholds; bases called with a non wild-type frequenon wild-typere attributed to noise, 30% to 70% are called heterozygous changes, and 90% to 100% are called homozygous changes.

Chromatograms were transferred to a Unix workstation, base called with PHRED (v.0.961028), assembled with PHRAP (v. 0.960731), scanned by POLYPHRED (v. 0.970312), and viewed with the CONSED program (v. 4.0).

Sequence reads were base called with Roche base caller version 2.5p1, and the sff files were converted to FASTQ files.