Discovering the Unknown: Improving Detection of Novel Species and Genera from Short Reads

Table 4

The table shows the distribution of top 10 most abundant species reads of PhymmBL and the top-8 species-reads passed the species resolution detectors for the red soudan acid mine drainage dataset, using the 635-genome training database.

(a)

PhymmBL
Organism	Matched reads
Gramella forsetii	4102
Marinobacter hydrocarbonoclasticus	3885
Flavobacterium johnsoniae	3480
Dinoroseobacter shibae	3402
Ruegeria pomeroyi	3119
Polaromonas naphthalenivorans	3116
Aeromonas salmonicida	2899
Rhodobacter sphaeroides	2616
Rhizobium leguminosarum	2541
Paracoccus denitrificans	2533

(b)

NBC detector		PhymmBL detector
Organism	Matched reads	Organism	Matched reads
Marinobacter hydrocarbonoclasticus	31	Dinoroseobacter shibae	85
Dinoroseobacter shibae	18	Marinobacter hydrocarbonoclasticus	62
Ruegeria sp. TM1040	17	Rhodobacter sphaeroides	24
Rhodobacter sphaeroides	15	Ruegeria pomeroyi	24
Shewanella sp. ANA-3	11	Ruegeria sp. TM1040	22
Shewanella baltica	5	Paracoccus denitrificans	20
Desulfotalea psychrophila	4	Shewanella baltica	17
Paracoccus denitrificans	4	Shewanella sp. ANA-3	14