Whole genome capture of vector-borne pathogens from mixed DNA samples: a case study of Borrelia burgdorferi

Carpi, Giovanna; Walter, Katharine S.; Bent, Stephen J.; Hoen, Anne Gatewood; Diuk-Wasser, Maria; Caccone, Adalgisa

doi:10.1186/s12864-015-1634-x

BMC Genomics

Table 1 Mapping statistics. For each sample the first four columns list the sample names followed by the capture reaction (number of genomic libraries captured in multiplex), the total number of sequenced bases (Mb) prior to filtering, and the percentage PCR duplicates. The final five columns report the capture efficiency (percentage of reads that mapped to the B. burgdorferi B31 reference genome), the percentage of sequence covered by at least one generated sequence read and the fold coverage (the total number of unique sequence reads which map to each nucleotide in the reference B31 genome) of filtered data for the linear chromosome (911 Kb) and the longest linear plasmid, lp54 (53 Kb), respectively

From: Whole genome capture of vector-borne pathogens from mixed DNA samples: a case study of Borrelia burgdorferi

Sample	Capture reaction	Sequenced bases (Mb)	% duplicate	Capture efficiency	% Chr covered	Coverage depth (Chr)	% lp54 covered	Coverage depth (lp54)
Bbcap1	20	34.22	42.63	0.44	99	11.71	98	12.77
Bbcap2_L1^a	10	108.45	50.1	0.64	100	52.92	100	52.53
Bbcap2_L2^b	4	237.68	70.49	0.61	100	109.52	100	113.51
Bbcap3	20	94.32	56.52	0.76	100	52.6	100	59.7
Bbcap4_L1	1	2066.79	92.57	0.10	100	140.83	98	194.75
Bbcap4_L2	4	188.60	61.81	0.56	100	76.92	100	94.68
Bbcap5	20	163.28	61.93	0.81	100	109.28	100	66.03
Bbcap6_L1	10	334.98	69.68	0.81	100	217.77	98	208.67
Bbcap6_L2	20	202.09	64.25	0.81	100	131.54	98	125.66
Bbcap7	20	75.67	55.01	0.65	100	39.08	98	34.93
Bbcap8	20	41.28	47.49	0.49	100	13.87	100	18.71
Bbcap9	10	221.18	67.38	0.76	99	134.32	98	148.14
Bbcap10	20	449.34	81.21	0.91	100	305.33	100	259
Bbcap12	20	185.23	67.57	0.77	100	103.49	98	91.28
Bbcap13	10	617.48	83.63	0.81	100	331.14	98	327.07
Bbcap14	20	140.75	62.89	0.70	100	76.99	98	86.69
Bbcap15	10	69.67	49.41	0.43	99	23.64	99	33.1
Bbcap16	20	119.57	54.98	0.72	99	71.59	99	71.73
Bbcap17	20	344.88	72.98	0.84	100	219.8	100	245.4
Bbcap19	10	53.31	41.46	0.53	100	19.73	100	25.17
Bbcap20	20	128.15	59.07	0.72	100	72.48	100	84.78
Bbcap21	20	135.54	60.87	0.71	99	72.32	98	79.68
Bbcap22	4	976.61	91.94	0.88	100	597.31	100	782.62
Bbcap23	20	159.50	63.51	0.64	99	77.6	98	105.44
Bbcap24	20	84.34	49.5	0.65	100	42.99	100	29.66
Bbcap25	20	61.60	50.95	0.50	99	25.13	98	28.68
Bbcap26	20	75.92	57.04	0.53	99	30.63	98	31.59
Bbcap27	20	73.49	60.97	0.59	100	33.45	100	35.05
Bbcap28	20	123.64	65.07	0.73	100	72.31	99	61.74
Bbcap29	10	255.63	72.17	0.86	100	167.46	100	178.06
Bbcap30_L1	10	343.08	70.18	0.83	100	225.25	99	183.62
Bbcap30_L2	4	825.19	88.1	0.79	100	520.17	100	438.71
Bbcap31_L1	10	292.77	65.76	0.85	100	198.23	100	136.51
Bbcap31_L2	20	232.33	66.08	0.85	100	156.58	100	109.34
Bbcap32	10	164.70	60.74	0.74	99	87.35	98	104.07
Sh834 ^c	Shotgun	9954.53	19.92	6.00E–05	7.7	1.2	0.8	1.23
Sh1589	Shotgun	825.75	18.15	1.40E–04	27.1	1.389	38	1.5

^aL1: Samples (indexed genomic libraries after capture) that were sequenced in a half lane
^bL2: Samples (indexed genomic libraries after capture) that were sequenced in a different half lane
^cSh: samples sequenced using shotgun approach

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ISSN: 1471-2164

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