Metagenomics of rumen bacteriophage from thirteen lactating dairy cattle

Ross, Elizabeth M; Petrovski, Steve; Moate, Peter J; Hayes, Ben J

doi:10.1186/1471-2180-13-242

BMC Microbiology

Table 1 Virome sequence volume, alignments and richness

From: Metagenomics of rumen bacteriophage from thirteen lactating dairy cattle

		Alignments to other viromes (%)						Richness by CatchAll
Sample	Data trimmed^T(Read pairs)	Cow 6993 [8]	Cow 7664 [8]	Cow 7887 [8]	Swine faeces [18]⁺	Human saliva [19]⁺	Pond [20]⁺	Best model^B	Estimated total species ± S.E.	Best discounted model^D	Estimated total species ± S.E.
Cow 2202^C	52,239,452	3.22	3.25	1.86	0.07	<0.01	<0.01	2MixedExp	5550786 ± 465864.1	SingleExp	18412.6 ± 1544.2
Cow 657	2,116,650	4.86	4.91	3.12	0.05	<0.01	<0.01	3MixedExp	4679342 ± 676180.6	2MixedExp	26795.8 ± 3871.9
Cow 1995	3,410,438	3.88	4.69	2.69	0.04	<0.01	<0.01	2MixedExp	5952188.7 ± 295239.5	SingleExp	5313.4 ± 263.5
Cow 2028	6,956,332	3.57	4.24	2.30	0.04	<0.01	<0.01	3MixedExp	6515260.9 ± 338382	2MixedExp	3369.8 ± 175
Cow 2042	4,048,214	3.19	3.71	2.22	0.03	<0.01	<0.01	2MixedExp	7904757.2 ± 622624.3	SingleExp	9023.1 ± 707.6
Cow 2165	4,362,890	4.57	5.14	3.20	0.04	<0.01	<0.01	4MixedExp	10353681.8 ± 119769.7	3MixedExp	1376492.9 ± 15923
Cow 3060	3,899,392	4.53	5.01	3.35	0.05	<0.01	<0.01	2MixedExp	5805999.9 ± 388938	SingleExp	11428.7 ± 765.5
Cow 4570	4,365,420	3.41	4.05	2.53	0.04	<0.01	<0.01	4MixedExp	22410379.6 ± 511083.2	3MixedExp	4126756.3 ± 94113.3
Cow 5679	3,681,922	3.70	4.84	2.67	0.04	<0.01	<0.01	3MixedExp	6098575.2 ± 404293.2	2MixedExp	6772.1 ± 448.5
Cow 6833	3,455,882	3.58	4.18	2.55	0.05	<0.01	<0.01	3MixedExp	7427673 ± 2447886.4	2MixedExp	30174.7 ± 9943.8
Cow 6857	8,998,900	4.18	4.71	2.77	0.04	<0.01	<0.01	3MixedExp	7916340 ± 2025360.6	2MixedExp	23466.2 ± 6003
Cow 6870	3,906,564	4.49	5.88	3.60	0.03	<0.01	<0.01	2MixedExp	4794540.3 ± 304303.4	SingleExp	13438.6 ± 852.7
Cow 7939	5,119,322	3.45	5.02	2.84	0.03	<0.01	<0.01	2MixedExp	6757358.4 ± 455261	SingleExp	7504.3 ± 495.6
Average*	8,197,029	3.89	4.59	2.75	0.04	<0.01	<0.01	-	7,858,991	-	435,304

*Average of all samples from this study.
^CCannulated animal.
^TAmount of sequence remaining after removal of poor quality bases.
⁺Multiple samples from study combined.
^BBest Model as assessed by the CatchALL program.
^DBest Model that has been corrected using the assumption of overrepresented singletons.

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ISSN: 1471-2180

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