"Table S1. Copy number, RNPct, and sequencing results for NEB+MDA and SWGA enriched spiked samples",,,,,,,,,,,,,
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Sample,Enrichment methoda,T. pallidum genome copies/µl in spiked samples (pre-enrichment)b ,"RNPCt in spiked samples
 (pre-enrichment) ",T. pallidum genome copies/µl in spiked samples (post-enrichment)b,"RNPCt in spiked samples 
(post-enrichment) ",Number of raw read pairs,"Total number of read pairs  after human removal, adaptor trimming and quality assessment",Number of read pairs classified as T. pallidumc,Percent of the read pairs classified as T. pallidumc,Mean Read Depthc,Percent of genome covered ?1Xc,Percent of genome covered ?5Xc,Percent of genome covered ?10Xc
"NEB+MDA_1:10,000_rep1",NEB+MDA,1.5,24.95,726,30.81,"22,987,457.00","12,847,858.00","1,643.00",0.01,0.67,20.27,4.98,0.93
"NEB+MDA_1:10,000_rep2",NEB+MDA,1.4,24.98,110,31.16,"21,168,862.00","11,669,225.00","1,266.00",0.01,0.51,14.95,3.64,0.87
"NEB+MDA_1:10,000_rep3",NEB+MDA,1.8,25.1,"2,056.00",32.29,"18,995,197.00","10,345,644.00","1,885.00",0.02,0.76,22.69,5.78,0.85
"NEB+MDA_1:1,000_rep1",NEB+MDA,12.9,25,"11,871.00",29.99,"28,397,459.00","13,544,664.00","43,634.00",0.32,18.17,79.46,64.28,49.02
"NEB+MDA_1:1,000_rep2",NEB+MDA,13,25.07,"3,649.00",31.22,"16,048,959.00","9,009,594.00","3,160.00",0.04,1.28,36.68,9.89,1.12
"NEB+MDA_1:1,000_rep3",NEB+MDA,13.8,25.13,"10,448.00",32.03,"22,455,122.00","12,693,326.00","2,481.00",0.02,1,31.91,7.08,0.8
NEB+MDA_1:100_rep1,NEB+MDA,138.9,24.84,"148,316.00",31.3,"12,130,073.00","7,325,455.00","33,199.00",0.45,13.77,99.93,95.18,71.49
NEB+MDA_1:100_rep2,NEB+MDA,111.8,25.1,"131,899.00",29.38,"23,117,357.00","15,576,108.00","93,578.00",0.6,39.39,99.99,99.9,99.34
NEB+MDA_1:100_rep3,NEB+MDA,137.6,24.82,"104,883.00",30.06,"21,990,019.00","11,031,554.00","39,001.00",0.35,16.48,99.73,96.81,81.6
NEB+MDA_1:10_rep1,NEB+MDA,"1,005.70",25.02,"779,820.00",30.25,"22,900,903.00","11,355,458.00","197,512.00",1.74,83.37,99.99,99.98,99.97
NEB+MDA_1:10_rep2,NEB+MDA,"1,035.40",25.12,"852,750.00",31.41,"22,840,971.00","11,365,682.00","212,416.00",1.87,89.72,99.99,99.99,99.98
NEB+MDA_1:10_rep3,NEB+MDA,"1,008.90",25.03,"721,630.00",31.79,"20,088,396.00","9,951,961.00","212,200.00",2.13,89.52,99.99,99.99,99.98
NEB+MDA_neat_rep1,NEB+MDA,"10,497.30",25.15,"7,216,300.00",29.7,"17,256,708.00","11,262,434.00","1,185,242.00",10.52,501.75,99.99,99.99,99.99
NEB+MDA_neat_rep2,NEB+MDA,"10,955.50",25.03,"6,468,500.00",30.88,"17,065,993.00","11,392,200.00","1,096,610.00",9.63,464.28,99.99,99.99,99.99
NEB+MDA_neat_rep3,NEB+MDA,"11,745.70",25.03,"6,334,100.00",27.26,"15,369,076.00","10,138,586.00","889,993.00",8.78,375.86,99.99,99.99,99.99
"SWGA_1:10,000_rep1",SWGA,1.5,24.95,"2,438,800.00",28.67,"23,192,918.00","15,017,442.00","393,396.00",2.62,164.85,49.68,34.98,29.47
"SWGA_1:10,000_rep2",SWGA,1.4,24.98,"363,200.00",28.44,"23,266,163.00","14,875,744.00","157,531.00",1.06,65.82,52.39,37.1,31.86
"SWGA_1:10,000_rep3",SWGA,1.8,25.1,"513,900.00",28.85,"27,225,312.00","16,590,056.00","162,696.00",0.98,68.03,61.2,43.3,36.01
"SWGA_1:1,000_rep1",SWGA,12.9,25,"3,692,900.00",28.58,"24,424,928.00","15,208,623.00","3,738,326.00",24.58,799.43,98.37,93.97,89.49
"SWGA_1:1,000_rep2",SWGA,13,25.07,"5,512,300.00",28.88,"28,291,268.00","18,868,094.00","5,334,480.00",28.27,"2,067.50",99.75,98.87,98.35
"SWGA_1:1,000_rep3",SWGA,13.8,25.13,"4,564,500.00",28.9,"30,982,443.00","22,497,319.00","4,697,593.00",20.88,"1,746.35",98.59,93.5,88.94
SWGA_1:100_rep1,SWGA,138.9,24.84,"14,364,100.00",28.94,"31,426,441.00","25,124,204.00","14,672,298.00",58.4,"4,123.81",99.99,99.99,99.98
SWGA_1:100_rep2,SWGA,111.8,25.1,"18,046,200.00",29.13,"30,783,339.00","24,372,409.00","14,780,695.00",60.65,"3,997.63",99.99,99.98,99.97
SWGA_1:100_rep3,SWGA,137.6,24.82,"13,604,500.00",29.28,"30,984,647.00","25,453,153.00","13,520,963.00",53.12,"4,161.87",99.99,99.99,99.98
SWGA_1:10_rep1,SWGA,"1,005.70",25.02,"22,526,900.00",29.29,"23,096,970.00","19,307,311.00","15,069,745.00",78.05,"4,519.92",99.99,99.99,99.99
SWGA_1:10_rep2,SWGA,"1,035.40",25.12,"18,365,400.00",29.3,"26,561,373.00","22,049,992.00","16,534,836.00",74.99,"4,705.41",99.99,99.99,99.99
SWGA_1:10_rep3,SWGA,"1,008.90",25.03,"20,287,300.00",29.5,"27,880,619.00","23,642,629.00","17,965,729.00",75.99,"4,888.72",99.99,99.99,99.99
aAll sequencing were performed using NovaSeq 6000; bBased on T. pallidum polA calculated copies/µl; cCalculated after quality assessment and T. pallidum selection of reads.,,,,,,,,,,,,,