Alignment Statistics

Table 5 | Alignment count statistics

Metric	Count	% of total	% of aligned
Total reads	{{ stats.aln.num_total_reads\|show_int }}	100%	{{ stats.aln.num_total_reads\|show_pct(stats.aln.num_aligned_reads) }}
Reads aligned	{{ stats.aln.num_aligned_reads\|show_int }}	{{ stats.aln.num_aligned_reads\|show_pct(stats.aln.num_total_reads) }}	100%
Reads aligned properly	{{ stats.aln.num_aligned_reads_proper_pairs\|show_int }}	{{ stats.aln.num_aligned_reads_proper_pairs\|show_pct(stats.aln.num_total_reads) }}	{{ stats.aln.num_aligned_reads_proper_pairs\|show_pct(stats.aln.num_aligned_reads) }}
Total bases	{{ stats.aln.num_total_bases\|show_int }}	100%	{{ stats.aln.num_total_bases\|show_pct(stats.aln.num_aligned_bases) }}
Bases aligned	{{ stats.aln.num_aligned_bases\|show_int }}	{{ stats.aln.num_aligned_bases\|show_pct(stats.aln.num_total_bases) }}	100%

Table 6 | Insert size statistics

Median	{{ stats.ins.median_insert_size\|show_int }}
Median absolute deviation	{{ stats.ins.median_absolute_deviation\|show_int }}
Maximum	{{ stats.ins.max_insert_size\|show_int }}
Minimum	{{ stats.ins.min_insert_size\|show_int }}

Table 7 | Other alignment statistics

Strand balance	{{ stats.aln.strand_balance\|show_float('.4g') }}
Mismatch rate	{{ stats.aln.rate_mismatch\|show_float('.2e') }}
Indel rate	{{ stats.aln.rate_indel\|show_float('.2e') }}