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Table 1 Whole-genome capture of B. microti from mixed DNA templates of tick and human samples

From: Babesia microti from humans and ticks hold a genomic signature of strong population structure in the United States

Sample Site State Collection year Source B. microti genome copiesa Capture efficiency Reference covered (%) Mean Chr coverage Mean apicoplast coverage
CT14-14 Mansfield CT 2014 human blood 685,844 98.45 98.9 1937.3 1322.2
N11-23 Nantucket MA 2011 human blood 164,819 97.75 98.8 1808.0 2168.8
N11-46 Nantucket MA 2011 human blood 81,207 97.49 98.8 1402.1 1291.3
ME14-04 Portland ME 2014 human blood 389,507 97.15 98.8 1071.0 714.8
ME13-07 Portland ME 2013 human blood 136,878 96.14 98.8 480.0 202.0
N14-18 Nantucket MA 2014 human blood 136,892 95.92 98.8 758.5 444.8
CT14-17 Mansfield CT 2014 human blood 118,180 95.78 98.7 216.3 134.6
NY-1509 Mashomack Preserve NY 2011 nymphal tick 22,259 95.53 98.7 176.5 598.8
CT-1807 Barn Island WMA CT 2013 nymphal tick NA 70.87 98.7 195.5 889.0
MA-2296 Quashnet River State Park MA 2013 nymphal tick 9931 69.41 98.7 312.4 1003.2
N-1725 Squam Swamp MA 2013 nymphal tick 6919 91.76 98.6 246.4 1135.4
N14-004 Nantucket MA 2014 human blood 67,064 88.46 98.5 112.6 133.9
N14-8 Nantucket MA 2014 human blood 1700 84.53 98.4 74.7 69.8
NY-1477 Connetquot State Park NY 2011 nymphal tick NA 80.66 98.4 63.6 105.1
WI-205 Black River State Forest WI 2011 nymphal tick NA 45.91 97.9 43.8 107.7
N-1729 Squam Swamp MA 2013 nymphal tick NA 48.11 97.0 33.8 173.1
NY-1468 Connetquot State Park NY 2011 nymphal tick 2314 16.26 96.4 26.5 69.0
NY-2455 James Baird State Park NY 2011 nymphal tick NA 66.68 95.8 26.4 58.1
MA-1689 Manuel F. Correllus State Forest MA 2013 nymphal tick 2256 86.12 94.8 34.3 248.6
MA-2473 Nickerson State Park MA 2013 nymphal tick 4904 84.35 93.7 22.5 23.6
NH-2440 Great Bay National Wildlife Refuge NH 2011 nymphal tick 7454 58.49 93.6 35.4 67.3
NY-2464 James Baird State Park NY 2011 nymphal tick NA 43.7 92.3 20.5 44.0
N11-15 Nantucket MA 2011 human blood 2218 65.07 90.0 18.9 12.8
CT14-1 Woodbridge CT 2014 human blood 8,025 85.84 81.9 15.4 11.0
WI-197 Black River State Forest WI 2011 nymphal tick NA 46.74 74.0 14.2 7.9
NY-2539 Hither Hills State Park NY 2013 nymphal tick NA 3.25 8.6 33.0 23.2
NY-2458 James Baird State Park NY 2013 nymphal tick 3191 81.95 4.5 4.2 4.3
MA-1670 Manuel F. Correllus State Forest MA 2013 nymphal tick NA 20.06 2.2 1.2 63.5
CT-2493 Rocky Neck SP CT 2013 nymphal tick NA 5.97 2.1 0.6 8.0
NY-2387 Ward Pound Ridge NY 2013 nymphal tick 268 17.22 1.9 0.4 7.0
NY-1524 Montauk Point State Park NY 2013 nymphal tick 59 8.48 1.9 0.4 9.3
RI-2584 Block Island RI 2013 nymphal tick NA 20.69 1.7 3.1 21.7
ME-2737 Cape Elizabeth ME 2013 nymphal tick 324 10.63 1.6 0.3 6.0
MA-2678 Nickerson State Park MA 2013 nymphal tick NA 2.68 1.5 0.3 8.0
CT-1824 Barn Island WMA CT 2013 nymphal tick 224 38.53 1.1 2.8 8.8
NJ-2719 Naval Weapons Station Earle NJ NA nymphal tick 118 31.21 1.1 2.1 17.1
NY-1587 Mashomack Preserve NY 2013 nymphal tick NA 22.26 0.8 2.6 8.9
RI-2589 Robins Hollow RI 2013 nymphal tick 105 5.99 0.6 0.2 9.2
CT-2413 50-Foot Cliff CT 2013 nymphal tick 200 14.05 0.4 0.0 2.0
WI-A406 Jackson County WI NA female adult tick NA 39.53 0.4 0.6 0.4
CT-2498 Rocky Neck SP CT 2013 nymphal tick NA 19.22 0.2 0.0 0.4
NY-2600 Hither Hills State Park NY 2013 nymphal tick 15 0.31 0.2 0.3 6.4
WI-A118 Spooner Veterinary Clinic, Washburn Co. WI NA female adult tick NA 3.74 0.1 0.2 2.0
WI-A424 Jackson County WI NA female adult tick NA 15.44 0.1 0.0 0.2
  1. Sample name, sampling site, state, collection year, source (nymphal or female adult I. scapularis tick or human blood), q-qPCR determined B. microti genome copy number, mean capture efficiency (the proportion of sequence reads mapping to B. microti R1 reference genome, GCF_000691945.1) percentage of genome covered (genome size 6.4 Mb), mean chromosomal coverage and mean apicoplast coverage (genome size 28.7 Kb). Samples are ranked by percentage of reference genome covered. The first 25 B. microti samples with at least 74 % coverage of the reference genome at minimum read depth of 10X were further used for downstream analyses
  2. aFor each sample, q-PCR determined B. microti genome copy number are shown for two techinical replicates