Artificial and natural duplicates in pyrosequencing reads of metagenomic data

Niu, Beifang; Fu, Limin; Sun, Shulei; Li, Weizhong

doi:10.1186/1471-2105-11-187

BMC Bioinformatics

Table 1 Genome projects with full genomes from Refseq and pyrosequencing reads from Short Read Archive

From: Artificial and natural duplicates in pyrosequencing reads of metagenomic data

ID^a	SRA Study^a	SRA Run^a	Platform	Genome	Genome size (Mbp)	GC (%)	Number reads	Read Density^b	% of total Duplicates	% of natural Duplicates (σ ^d)
20067	SRP000091	SRR000351	GS_20	NC_010741	1.13946	52	529181	0.4644	13.585	5.032	(0.030)
20739	SRP000868	SRR017616	GS_FLX	NC_013170	1.61780	50	513712	0.3175	17.751	4.999	(0.022)
29525	SRP000571	SRR013433	GS_FLX	NC_013124	2.15816	68	570098	0.2641	9.938	4.464	(0.034)
19265	SRP000036	SRR000223	GS_20	NC_010085	1.64526	34	429372	0.2609	12.120	4.418	(0.026)
19981	SRP000204	SRR001584	GS_20	NC_010830	1.88436	35	399515	0.2120	26.027	4.293	(0.030)
20655	SRP000207	SRR001568	GS_20	NC_012803	2.50109	72	528437	0.2112	9.734	4.099	(0.032)
20833	SRP000867	SRR017612	GS_FLX^e	NC_013174	2.74965	58	574027	0.2087	16.266	3.745	(0.027)
18819	SRP000035	SRR000219	GS_20	NC_009637	1.77269	33	332809	0.1877	15.145	3.664	(0.024)
29443	SRP000895	SRR017790	GS_FLX	NC_013166	2.85207	43	529344	0.1855	16.017	3.044	(0.025)
29419	SRP000560	SRR013388	GS_FLX	NC_012785	2.30212	41	416146	0.1807	9.537	3.025	(0.031)
19543	SRP000205	SRR001565	GS_20	NC_010483	1.87769	46	321938	0.1714	25.373	2.886	(0.038)
29381	SRP000558	SRR013382	GS_FLX	NC_011832	2.92292	55	461295	0.1578	8.526	2.911	(0.024)
29403	SRP000584	SRR013477	GS_FLX	NC_013162	2.61292	39	400460	0.1532	11.796	2.549	(0.021)
29177	SRP000442	SRR007446	GS_FLX	NC_011901	3.46455	65	438386	0.1265	14.140	2.239	(0.023)
29493	SRP000569	SRR013431	GS_FLX	NC_011883	2.87344	58	362855	0.1262	11.171	2.204	(0.023)
29175	SRP000928	SRR018125	GS_FLX	NC_011661	1.85556	33	225795	0.1216	6.209	2.151	(0.021)
27731	SRP000397	SRR006411	GS_FLX	NC_011769'	4.04030	67	488823	0.1209	18.793	2.073	(0.020)
31289	SRP000919	SRR018042	GS_FLX	NC_012917	4.86291	51	517593	0.1064	3.211	1.948	(0.037)
20635	SRP000049	SRR000266	GS_20	NC_011666	4.30543	63	401125	0.0931	10.364	1.943	(0.022)
31295	SRP000921	SRR018051	GS_FLX	NC_012912	4.81385	54	441287	0.0916	6.938	1.941	(0.019)
29527	SRP000893	SRR017783	GS_FLX	NC_013173	3.94266	58	352814	0.0894	8.356	1.926	(0.022)
20039	SRP000209	SRR001574	GS_FLX^f	NC_010524	4.90940	68	422674	0.0860	8.566	1.785	(0.023)
19701	SRP000046	SRR000255	GS_20	NC_010644	1.64356	39	136514	0.0830	5.922	1.744	(0.022)
19743	SRP000045	SRR000254	GS_20	NC_011145	5.06163	74	409136	0.0808	7.464	1.739	(0.019)
20095	SRP000054	SRR000278	GS_20	NC_011891	5.02933	74	404796	0.0804	8.363	1.515	(0.022)
30681	SRP000922	SRR018054	GS_FLX	NC_012947	4.57094	50	367491	0.0803	11.324	1.449	(0.018)
21119	SRP000208	SRR001573	GS_FLX^f	NC_012032	5.26895	56	392222	0.0744	10.026	1.321	(0.025)
18637	SRP000034	SRR000215	GS_20	NC_010172	5.47115	68	395973	0.0723	12.998	1.306	(0.016)
20167	SRP000053	SRR000277	GS_20	NC_011004	5.74404	64	413261	0.0719	14.572	1.248	(0.022)
19989	SRP000211	SRR001579	GS_20	NC_010571	5.95761	65	378824	0.0635	5.484	1.145	(0.023)
19449	SRP000043	SRR000248	GS_20	NC_011768	6.51707	54	395672	0.0607	16.631	1.108	(0.018)
33873	SRP000554	SRR013372	GS_FLX	NC_012691	3.47129	49	191873	0.0552	43.680	1.001	(0.025)
27951	SRP000587	SRR013487	GS_FLX	NC_013132	9.12735	45	496792	0.0544	15.017	0.283	(0.033)
20827	SRP000582	SRR013470	GS_FLX	NC_012669	4.66918	73	246279	0.0527	4.140	0.295	(0.023)
33069	SRP000920	SRR018045	GS_FLX	NC_012880	4.67945	55	226208	0.0483	13.585	5.032	(0.030)
19705	SRP000576	SRR013446	GS_FLX	NC_013093	8.24814	73	381851	0.0462	17.751	4.999	(0.022)
29975	SRP000443	SRR013137	GS_FLX	NC_011992	3.79657	66	161655	0.0425	9.938	4.464	(0.034)
17265	SRP000067	SRR000311	GS_20	NC_008369	1.89572	32	28221	0.0148	12.120	4.418	(0.026)
20729	SRP000267	SRR004103	GS_FLX	NC_012918	4.74581	60	22822	0.0048	26.027	4.293	(0.030)

^aProject IDs, SRA study accessions, and SRA run accessions are from NCBI Short Read Archive at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi.
^bRead Density is the number of reads divided by the genome length.
^dσ is the standard deviation, which is based on the results of 100 simulations (see the "Duplicated reads of genomic datasets" section).
^eThe platform provided by SRA is GS_FLX, and the read length (~400 bp) suggests GS_FLX Titanium.
^fThe platform provided by SRA is GS_20, but the read length (~200 bp) suggests GS_FLX.

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ISSN: 1471-2105

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