Table 4 RNA-seq mapping on L. chalumnae genome statistics

Mapping on annotated genes

Counted fragments

21,589,809 (48.59%)

Uncounted fragments

22,846,398 (51.41%)

Match specificity

98.1%

Reads mapped in pairs

43,179,618 (48.59%)

Reads mapped in broken pairs

11,603,481 (13.06%)

Unmapped reads

34,089,315 (38.36%)

Fragments mapped on exon-exon junctions

11,147,648 (51.63%)

Fragments mapped on exon-intron junctions

642,299 (2.98%)

Total fragments mapped on exons

20,084,744 (93.03%)

Total fragments mapped on introns

1,505,065 (6.97%)

Mapping on genomic scaffolds

Total number of reads mapping on genomic scaffolds

85,682,920 (96.41%)

Reads mapped on non-annotated genes

30,899,821 (34.77%)

Unmapped reads

3,189,494 (3.59%)