Construction of a virtual Mycobacterium tuberculosis consensus genome and its application to data from a next generation sequencer

Okumura, Kayo; Kato, Masako; Kirikae, Teruo; Kayano, Mitsunori; Miyoshi-Akiyama, Tohru

doi:10.1186/s12864-015-1368-9

Table 6 Comparison of Illumina read mapping efficacy using clinical isolates derived from different lineages using

From: Construction of a virtual Mycobacterium tuberculosis consensus genome and its application to data from a next generation sequencer

Isolate	Lineage		H37Rv			Consensus sequence			Subtraction of ratio (%)
		Mapping stringency*	Ambiguity	Medium	Strict	Ambiguity	Medium	Strict	(Consensus-H37Rv)
F092	EAI	mapped	676219	676007	674779	677079	676941	676114
		unmapped	20275	20487	21715	19415	19553	20380
		ratio (%)	97.089	97.059	96.882	97.212	97.193	97.074	0.123	0.134	0.192
J156	EAI	mapped	1656675	1656191	1652024	1661496	1660887	1657869
		unmapped	37151	37635	41802	32330	32939	35957
		ratio (%)	97.807	97.778	97.532	98.091	98.055	97.877	0.285	0.277	0.345
F038	Haarlem, LAM, X etc.	mapped	985717	985256	978713	986844	986318	980541
		unmapped	43761	44222	50765	42634	43160	48937
		ratio (%)	95.749	95.704	95.069	95.859	95.808	95.246	0.109	0.103	0.178
F070	Haarlem, LAM, X etc.	mapped	847048	846879	844774	847486	847257	845485
		unmapped	21212	21381	23486	20774	21003	22775
		ratio (%)	97.557	97.537	97.295	97.607	97.581	97.377	0.05	0.044	0.082
J073	Haarlem, LAM, X etc.	mapped	1511361	1511205	1508937	1512926	1512725	1511328
		unmapped	25005	25211	27479	23490	23691	25088
		ratio (%)	98.372	98.359	98.211	98.471	98.458	98.367	0.099	0.099	0.156
J147	Haarlem, LAM, X etc.	mapped	835484	835319	834077	835192	834976	834227
		unmapped	14694	14859	16101	14986	15202	15951
		ratio (%)	98.272	98.252	98.106	98.237	98.212	98.124	−0.034	−0.04	0.018
F081	other non-Beijing	mapped	984775	984303	981542	986321	986079	983479
		unmapped	31067	31539	34300	29521	29763	32363
		ratio (%)	96.942	96.895	96.623	97.094	97.07	96.814	0.152	0.175	0.191
J020	other non-Beijing	mapped	1061748	1061460	1059770	1063613	1063346	1062167
		unmapped	22918	23206	24896	21053	21320	22499
		ratio (%)	97.887	97.861	97.705	98.059	98.034	97.926	0.172	0.174	0.221
J027	other	mapped	741045	740904	739801	742516	742329	741694
	non-Beijing	unmapped	13721	13862	14965	12250	12437	13072
		ratio (%)	98.182	98.163	98.017	98.377	98.352	98.268	0.195	0.189	0.251
F022	Ancestral Beijing	mapped	1140373	1140107	1137877	1145147	1144862	1143607
		unmapped	32673	32939	35169	27899	28184	29439
		ratio (%)	97.215	97.192	97.002	97.622	97.597	97.49	0.407	0.405	0.488
J090	Ancestral Beijing	mapped	2087545	2086983	2082777	2095411	2094879	2092249
		unmapped	47551	48113	52319	39685	40217	42847
		ratio (%)	97.773	97.747	97.55	98.141	98.116	97.993	0.368	0.37	0.444
J002	Ancestral Beijing	mapped	725501	725308	724182	727822	727702	727147
		unmapped	13427	13620	14746	11106	11226	11781
		ratio (%)	98.183	98.157	98.004	98.497	98.481	98.406	0.314	0.324	0.401
J029	Modern Beijing	mapped	935765	935598	934129	939368	939185	938425
		unmapped	21607	21774	23243	18004	18187	18947
		ratio (%)	97.743	97.726	97.572	98.119	98.1	98.021	0.376	0.375	0.449
F076	Modern Beijing	mapped	523546	523438	522478	526300	526150	525618
		unmapped	17480	17588	18548	14726	14876	15408
		ratio (%)	96.769	96.749	96.572	97.278	97.25	97.152	0.509	0.501	0.58
J111	Modern Beijing	mapped	703968	703761	702412	708028	707765	707024
		unmapped	17244	17451	18800	13184	13447	14188
		ratio (%)	97.609	97.58	97.393	98.172	98.135	98.033	0.563	0.555	0.639
ii) Comparison of mappping frequency ratio (%) among the MTBC lineanges
		EAI	HaarlemLAM, X etc.	other non-Beijing
	Haarlem,LAM, X etc.	ns	-	-
	non-Beijing	ns	ns	-
	Beijing	P<0.05	P<0.01	P<0.05

In this analysis CS based on 13 M. tuberculosis strains (Table 1) was used as the consensus sequence. i) The effects on mapping efficacy were tested for three combinations of parameters: mismatch cost, insertion cost, deletion cost, matching length and similarity. *Mapping stringency was defined as Ambiguous, with frequencies of mismatch cost, insertion cost, deletion cost, matching length and similarity of 2, 2, 2, 0.5, and 0.8, respectively; Medium, with frequencies of 2, 3, 3, 0.5, and 0.8, respectively; and Strict, with frequencies of 3, 3, 3, 0.5, and 0.95, respectively. Significant differences in mapping frequencies were assessed using multiple comparisons of proportions tests [44]. For all isolates, the difference between H37Rv and CS as a reference differed significantly (p < 0.0001). For each stringency setting, the ratio of mapped to total reads was calculated, and these values used to calculate differences in mapping frequency between the consensus and H37Rv sequences by simple subtraction.
ii) Based on the difference in mapping frequency in 1), the mapping frequencies of MTBC lineages were compared using Mann–Whitney U tests. The Haarlem, LAM, X and Beijing sequences showed the greatest difference (p < 0.01) in mapping frequencies when compared relative to the consensus and H37Rv sequences.

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ISSN: 1471-2164

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