Table 1

Effect of filter threshold setting on best match lineages for E. coli

Filter threshold setting


0%
 2%
 5%
 10%
 20%
 30%
 40%
 60%
 80%
 100%
Enterobacteria
 4,000
 4,034
 4,052
 4,063
 4,064
 4,078
 4,092
 4,105
 4,112
 4,112
Other bacteria
 132
 112
 103
 96
 85
 74
 76
 64
 58
 58
Phage
 27
 24
 18
 14
 12
 11
 7
 6
 6
 6
Eukaryotes
 8
 6
 6
 6
 4
 4
 4
 4
 3
 3
Archaea
 0
 0
 0
 0
 0
 0
 0
 0
 0
 0
Total matches
 4,167
 4,176
 4,179
 4,179
 4,165
 4,167
 4,179
 4,179
 4,179
 4,179

As discussed in the text, a zero percent filter threshold setting retains only candidates with bit scores equal to the top non-self blast match. A setting of 100% retains all matches as candidates for subsequent LPI calculations. Some columns have slightly lower total numbers due to matches with uncultured organisms, which contain no lineage information but were not filtered out in this experiment.

Podell and Gaasterland Genome Biology 2007 8:R16   doi:10.1186/gb-2007-8-2-r16

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