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Table 2 Annotation summary for example dataset

From: WebMGA: a customizable web server for fast metagenomic sequence analysis

Tool Annotation Summarya
FNA-stat Total reads: 555853, Length: 45~607, Average length: 251, Total bases: 139813458, Total ambiguous bases: 96190, Distribution of GC% and length in text files and in graphic files similar to Figure 2d
CD-HIT-EST Parameters: "-d 0 -n 10 -l 11 -r 1 -p 1 -g 1 -G 0 -c 0.95 -aS 0.8" Clusters: 419802, Size of the largest cluster: 69, Clusters in CD-HIT format and in 'TAB' delimited text file, Distribution of clusters in graphic file similar to Figure 2b
HMM-rRNA rRNA sequences identified: 3858, Archaeal-16S: 1, Eukaryotic-18S: 3, Bacterial-16S: 1347, Bacterial-5S: 220, Bacterial-23S: 2285, Archaeal-5S: 2
tRNA-SCAN tRNA sequences identified: 1378
Metagene ORFs: 571261
FAA-stat Total ORFs: 555853, Length: 20-121, Average length: 66, Total letters: 37859696, Total ambiguous letters: 87294, Distribution length in text file and in graphic file similar to Figure 2d
CD-HIT Parameters: "-d 0 -n 5 -p 1 -g 1 -G 0 -c 0.9 -aS 0.8" Clusters: 396559, Size of the largest cluster: 154, Clusters in CD-HIT format and in 'TAB' delimited text file, Distribution of clusters in graphic file similar to Figure 2b
COG Parameters: "-e 0.001" Total alignments: 199002, Total ORFs aligned: 198933, Total COG families aligned: 2848, Total COG classes aligned: 23, Alignments and derived results in 'TAB' delimited text files similar to Figure 2c
PFAM Parameters: "-e 0.001" Total alignments: 187156, Total ORFs aligned: 174115, Total PFAM families aligned: 3131, Total ORFs with GO annotation: 123294, Total GO terms annotated: 964 Total ORFs with EC annotation: 46207, Total EC terms annotated: 319 Alignments and derived results in 'TAB' delimited text files similar to Figure 2c
TIGRFAM Parameters: "-e 0.001" Total alignments: 6357, Total ORFs aligned: 6172, Total PFAM families aligned: 327, Total ORFs with GO annotation: 3077, Total GO terms annotated: 252 Total ORFs with EC annotation: 564, Total EC terms annotated: 57 Alignments and derived results in 'TAB' delimited text files similar to Figure 2c
  1. a Detailed parameters are explained at WebMGA website.