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. Author manuscript; available in PMC: 2016 Feb 2.
Published in final edited form as: Curr Protoc Microbiol. 2015 Feb 2;36:9D.4.1–9D.4.20. doi: 10.1002/9780471729259.mc09d04s36

Table 1.

List of strains used for design of the SpSGH

Pneumococcal Strain Serotype MLST Genome (bp) #ORFs Location of isolation Carriage / disease Status Source Accession Number Technology Coverage
SP3 3 180 2033581 2177 Pittsburgh, US disease draft Ref. [4] AAZZ00000000 454 GS20 18x
SP6 6 460 2162916 2325 Pittsburgh, US disease draft Ref. [4] ABAA00000000 454 GS20 19x
SP9 9 1269 2117908 2241 Pittsburgh, US disease draft Ref. [4] ABAB00000000 454 GS20 20x
SP11 11 62 2060705 2127 Pittsburgh, US disease draft Ref. [4] ABAC00000000 454 GS20 17x
SP14 14 124 2148093 2624 Pittsburgh, US disease draft Ref. [4] ABAD00000000 454 GS20 16x
SP18 6 new 2105593 2211 Pittsburgh, US disease draft Ref. [4] ABAE00000000 454 GS20 19x
SP19 19 485 2136434 2301 Pittsburgh, US disease draft Ref. [4] ABAF00000000 454 GS20 16x
SP23 23 37 2103479 2200 Pittsburgh, US disease draft Ref. [4] ABAG00000000 454 GS20 15x
INV104B 1 227 2142122 1941 Oxford, UK disease complete Ref. [4] FQ312030 Sanger 9x
OXC141 3 180 2036967 1973 Oxford, UK carriage complete Ref. [4] FQ312027 Sanger 9x
INV200 14 9 2093318 2045 Oxford, UK disease complete Ref. [4] FQ312029 Sanger / Illumina 12x/85x
SpnATCC700669 23F 81 2221315 2132 Spain carriage complete Ref. [19] FM211187 Sanger 8x
Sp03_4156 3 180 2058353 1954 The Netherlands carriage draft Donati et al FQ312045 Sanger / 454 FLX 5x/25x
Sp03_4183 3 180 1993183 1933 The Netherlands carriage draft Donati et al FQ312043 Sanger / 454 FLX 6x/16x
Sp07_2838 3 180 1990038 1901 Bolivia carriage draft Donati et al CACI01000000 Sanger / 454 FLX 5x/23x
Sp99_4038 3 180 2010908 1952 Glasgow Reference Lab disease draft Donati et al FQ312041 Sanger / 454 FLX 7x/26x
Sp99_4039 3 180 2010104 1954 Glasgow Reference Lab disease draft Donati et al FQ312044 Sanger / 454 FLX 4x/32x
Sp02_1198 3 180 1989367 1938 Glasgow Reference Lab disease draft Donati et al CACH01000000 Sanger / 454 FLX 5x/28x
A45 3 New 2041833 1932 Newmarket disease draft Donati et al CACG01000000 Sanger / 454 FLX 6x/15x
P1041 1 217 2166490 1905 Ghana disease draft Donati et al CACE01000000 Sanger / 454 FLX /
Illumina		 5x/13x/96x
Sp03_2672 1 306 2144331 1904 Glasgow Reference Lab disease draft Donati et al FQ312039 Sanger / 454 FLX 5x/25x
Sp03_3038 1 306 2164519 1936 Glasgow Reference Lab disease draft Donati et al FQ312042 Sanger / 454 FLX 5x/20x
Sp06_1370 1 306 2012346 1874 Glasgow Reference Lab disease draft Donati et al CACJ01000000 Sanger / 454 FLX 5x/19x
NCTC7465 1 615 2100988 1845 Type strain, Rockefeller USA,
1948		 disease draft Donati et al CACF01000000 Sanger / 454 FLX /
Illumina		 5x/11x/86x
P1031 1 303 2111882 2073 Ghana disease complete Donati et al CP000920 Sanger / 454 FLX Finished*
D39 2 595 2046115 1914 US disease complete Ref. [17] CP000410 Sanger Finished*
TIGR4 4 205 2160842 2125 Norway disease complete Ref. [15] AE005672 Sanger Finished*
70585 5 289 2184682 2202 Bangladesh disease complete Donati et al CP000918 Sanger / 454 FLX Finished*
JJA 14 66 2120234 2123 Brazil disease complete Donati et al CP000919 Sanger / 454 FLX Finished*
MLV-016 11A 62 2247118 2159 USA, Europe carriage draft Donati et al ABGH00000000 Sanger / 454 FLX 9x/28x
CDC0288-04 12F 220 2051140 2105 USA, UK disease draft Donati et al ABGF00000000 Sanger / 454 FLX 10x/31x
CDC3059-06 19A 199 2293277 2379 Iceland, UK, USA, others disease draft Donati et al ABGG00000000 Sanger / 454 FLX 9x/26x
Hungary19A-6 19A 268 2245615 2155 Hungary disease complete Donati et al CP000936 Sanger / 454 FLX Finished*
Taiwan19F-14 19F 236 2112148 2044 Taiwan disease complete Donati et al CP000921 Sanger / 454 FLX Finished*
CDC1873-00 6A 376 2265195 2402 USA disease draft Donati et al ABFS00000000 Sanger / 454 FLX 9x/20x
670-6B 6B 90 2240045 2384 Spain disease complete Ref. [4] CP002176 Sanger Finished*
CDC1087-00 7F 191 2190853 2232 Bra, Den, Fin, Neth, Nor, UK,
Uru, USA		 disease draft Donati et al ABFT00000000 Sanger / 454 FLX 9x/14x
SP195 9V 156 2198294 2287 Worldwide disease draft Donati et al ABGE00000000 Sanger / 454 FLX 10x/29x
G54 19F 63 2078953 2115 Italy disease complete Ref. [4] CP001015 Sanger Finished*
R6 2 595 2038615 2043 Laboratory laboratory complete Ref. [16] AE007317 Sanger Finished*
ST13v1-CGSSp14BS292 14 13 2100368 2290 Children's Hospital of
Pittsburgh		 disease draft Hiller 2010 ABWQ00000000.1 454 FLX 21.5x
ST13v12-CGSSpBS293 NT 13 2065452 2242 Children's Hospital of
Pittsburgh		 disease draft Hiller 2010 ABWU00000000.1 454 FLX 23x
ST13v6-CGSSpBS457 NT 13 2053197 2225 Children's Hospital of
Pittsburgh		 disease draft Hiller 2010 ABWB00000000.1 454 FLX 27x
ST2011v4-CGSSpBS455 NT 2011 2086050 2182 Children's Hospital of
Pittsburgh		 disease draft Hiller 2010 ADHN00000000.1 454 FLX Titanium 28x
SV35-T23 23F 81 2156885 2242 AIDS clinic of St. Vincent's
Medical Center, Richmond,
New York, US		 disease draft Hiller,2011 ADNN01000000 454 FLX 26x
SV36-T3 3 81 2162633 2239 AIDS clinic of St. Vincent's
Medical Center, Richmond,
New York, US		 disease draft Hiller,2011 ADNO01000000 454 FLX 26x
PN4595-T23 23F 81 2169192 2259 Lisbon, Portugal carriage draft Hiller,2011 ABXO01 454 FLX 27.6x
CGSP14 14 15 2209198 2206 China, Beijing Institute of
Genomics		 disease complete Ref. [18] CP001033 Sanger Finished*
CCRI 1974 14 124 2005075 2074 McGill University, Canada disease draft Ref. [20] ABZC00000000 454 FLX 20x
CCRI 1974M2 14 124 2003231 2069 McGill University, Canada disease draft Ref. [20] ABZT00000000 454 FLX 20x
AP200 11A 62 2084139 2149 University of Siena, Italy disease draft Unpublished CP002121 454 10x