Polish with Reads report
An example of the first sections of the Polish with Reads summary report is shown in figure 6.2.
Figure 6.1: Polish with Reads report
The report contains the following information:
- Polishing summary
- Input sequences. Number of target input sequences.
- Input reads. Number of high-quality input reads.
- Alignments (includes multiple alignments). The number of alignments between target sequences and high-quality reads.
- Polished sequences. Number of sequences that were polished.
- Polished windows (%). The percentage of windows that were polished.
- Sequences. For each target input sequence, the following information is given:
- Name. Name of the sequence.
- Nucleotides. Number of nucleotides in the sequence.
- Mapped reads. Number of high-quality reads that mapped to the sequence.
- Polished windows (%). The percentage of windows that were polished.
- Sequence statistics
- Sequences. Number of sequences.
- Minimum, Maximum, Average. Minimum, maximum and average sequence length.
- N50. The length of the shortest sequence in sets of sequences of equal length or longer, where the summed length of sequences is at least 50% of the total sequence length.
- N90. The length of the shortest sequence in a set of sequences of equal length or longer, where the summed length of sequence is at least 90% of the total sequence length. N90 will be equal to or smaller than N50.
- Total. The number of bases in the sequences.
- Sequence length distribution. A graph depicting the number of sequences found at a specific length.