Table 1. Pyrosequencing metrics from raw data before and after standard MG-RAST quality control (QC) filters.

	Sequences	Base Pairs	Mean Length	Post QC Sequences	Post QC Base Pairs	Post QC Mean Length
Healthy 1	8,511	4,427,140	520±51	8,315	4,383,098	527±16
Healthy 2	6,579	3,415,612	519±54	6,356	3,357,920	528±16
Healthy 3	21,600	11,236,309	520±66	2,313	1,242,651	537±21
Healthy 4	16,573	8,694,983	524±51	16,292	8,644,714	530±15
Healthy 5	6,552	3,471,194	529±37	6,473	3,449,816	532±16
Healthy 6	17,593	9,238,535	525±60	17,027	9,107,355	534±15
Mean (±SD)	12,901(6,491)	6,747,296(3,387,243)		9,463(5,914)	5,030,926(3,154,244)
Colitis 1	7,446	3,806,461	511±79	7,445	3,805,868	511±79
Colitis 2	6,043	3,116,620	515±56	5,908	3,091,273	523±13
Colitis 3	6,164	3,161,864	512±52	5,907	3,085,726	522±22
Colitis 4	9,202	4,609,881	500±74	8,238	4,324,045	524±19
Colitis 5	13,370	6,666,805	498±91	12,540	6,523,300	520±14
Colitis 6	34,608	18,717,239	540±23	2,920	1,593,071	545±14
Colitis 7	7,869	4,286,601	544±20	7,822	4,258,982	544±12
Colitis 8	15,522	8,418,453	542±27	15,408	8,359,126	542±14
Colitis 9	8,705	4,677,368	537±19	8,619	4,626,452	536±12
Colitis 10	9,411	5,116,407	543±20	9,362	5,090,677	543±10
Mean (±SD)	11,834(8,549)	6,257,770(4,665,905)		8,417(3.511)	4,475,852(1,895,944)
Total	195,748	103,061,472		140,945	74,944,074

Total number of sequences, number of base pairs and the mean length of sequences (bp) present in the original fasta file before and after MG-RAST standard quality control filters. Means and standard deviations (±SD) among healthy horses and horses with colitis are also presented.