Table 1.

Read Statistics by Animal

ID	Diet	Total readsa	Reads with valid paired ORFsb	# (%) reads that hit to nodesc	# of reads hitting multiple nodes	# (%) reads hit to sheep genomed	#OTU founde
1003	FORG	16,779,099	14,521,805	271,571 (1.87%)	220,794	58,830 (0.35%)	109
1009	FORG	35,930,923	30,282,660	761,728 (2.52%)	548,931	1,855,867 (5.17%)	161
1127	FORG	41,120,479	35,920,407	570,177 (1.59%)	459,714	63,121 (0.15%)	137
1208	FORG	44,823,544	39,038,632	1,012,146 (2.59%)	790,442	18,155 (0.04%)	140
1248	FORG	22,698,997	19,869,280	673,066 (3.39%)	441,001	2,804 (0.01%)	127
1366	FORG	18,124,115	14,952,153	396,240 (2.65%)	275,291	42,582 (0.23%)	119
1397	FORG	32,221,706	28,176,562	657,645 (2.33%)	486,817	62,527 (0.19%)	137
7505	FORG	47,234,706	38,189,761	651,061 (1.70%)	478,999	1,175,563 (2.49%)	177
1026	CONC	29,835,213	24,169,312	642,601 (2.66%)	780,456	7,564 (0.03%)	108
1101	CONC	54,927,600	47,578,081	1,008,933 (2.12%)	1,059,980	44,188 (0.08%)	142
1111	CONC	26,710,771	23,016,865	362,506 (1.57%)	486,293	167,325 (0.63%)	137
1220	CONC	7,800,938	6,274,376	109,479 (1.74%)	126,946	1,226 (0.02%)	75
1239	CONC	42,216,924	36,551,070	751,236 (2.06%)	775,268	24,083 (0.06%)	138
1348	CONC	13,577,697	11,843,596	245,424 (2.07%)	246,823	12,233 (0.09%)	102
1396	CONC	18,274,753	15,860,653	278,963 (1.76%)	339,002	7,330 (0.04%)	124
7429	CONC	30,236,139	26,315,246	553,079 (2.10%)	537,174	65,498 (0.22%)	135

^aTotal paired reads sequenced prior to quality filtering

^bTotal number of paired reads passing read quality filtering and having a sufficiently long ORF in both members (Materials and Methods)

^cNumber and percent of valid reads (previous column) that were mapped to nodes according to our criteria (Materials and Methods)

^dNumber and percent of total reads that mapped to the sheep genome at 80% percent identity

^eNumber of distinct OTUs identified previously in these sequences [18]