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Table 1 Characteristics of the isolates sequenced in this study

From: Genomic epidemiology of Lineage 4 Mycobacterium tuberculosis subpopulations in New York City and New Jersey, 1999–2009

Isolate Lineage Location Year Reads Mean read depth %Genome coverage Filtered SNPs Genbank Accession
BE_116771 1 NJ 1999 2,883,388 31.633 0.994 2065 LKMF01000000
BE3_11657 3 NJ 1999 2,934,017 63.728 0.996 1046 LKDN01000000
001_13432 4 NYC 2000 3,027,826 75.362 0.996 1060 LKDO01000000
AH_14271 4 NYC 2001 4,045,981 95.556 0.998 1074 LKDP01000000
AH26_26663 4 NYC 2010 1,356,722 33.169 0.997 1044 LJIQ01000000
AH26_28866 4 S. Africa 2011 1,958,645 23.009 0.994 968 LKMH01000000
AU_8623 4 NYC 1998 6,294,738 71.734 0.996 983 LKMG01000000
BE_10225 4 NJ 1999 1,896,522 47.939 0.994 1049 LJIK01000000
BE_13443 4 NYC 2001 3,669,247 91.597 0.995 1071 LKDQ01000000
BE_14248 4 NYC 2001 2,921,250 70.22 0.995 1077 LKDR01000000
BE_7556 4 NJ 1997 3,580,176 41.681 0.995 961 LJIL01000000
C_913 4 NYC 1992 14,910,476 387.981 0.995 1101 LKMI01000000
C_10367 4 NYC 1999 2,082,141 51.722 0.995 1057 LJIP01000000
C_14229 4 NYC 2001 5,108,155 127.485 0.996 1128 LKDS01000000
C130 4 NYC 1991 2,704,576 64.086 0.996 1057 LJIN01000000
C24_20545 4 NYC 2005 2,856,851 71.852 0.997 1125 LJIM01000000
C28_9319 4 NJ 1998 2,179,814 53.922 0.995 1058 LJIO01000000
C28_9904 4 NJ 1999 1,632,080 39.971 0.994 1019 LJIR01000000
C30_19588 4 NYC 2004 4,631,768 115.895 0.996 1083 LKDT01000000
C34_13853 4 NYC 2001 2,008,488 48.272 0.995 1048 LKHH01000000
C4_16679 4 NYC 2002 3,966,004 96.262 0.996 1075 LKIF01000000
C49_20090 4 NYC 2005 1,966,774 47.421 0.995 1024 LKIG01000000
C53_20899 4 NYC 2006 3,105,243 74.778 0.994 1062 LKIH01000000
H_13559 4 NYC 2001 3,185,904 76.306 0.996 1041 LKII01000000
H_13571 4 NYC 2001 1,815,449 44.429 0.995 1021 LKIJ01000000
H_7300 4 NYC 1997 2,011,143 48.599 0.994 1020 LKDL01000000
H55_24991 4 NYC 2009 1,743,190 42.094 0.995 1041 LKIK01000000
H6_10443 4 NJ 1999 1,799,336 43.72 0.995 1019 LKIL01000000
H6_12226 4 NJ 2000 4,457,191 105.789 0.996 1074 LKIM01000000
H6_7420 4 NJ 1997 1,719,494 43.153 0.994 1041 LKDM01000000
I_15762 4 NYC 2002 2,785,341 66.101 0.995 1057 LKIN01000000
KI_19771 4 NYC 2004 2,884,815 69.225 0.995 1079 LKIO01000000
L_13621 4 NYC 2001 8,967,725 221.783 0.997 1098 LKIP01000000
V_13678 4 NYC 2001 1,517,250 35.643 0.997 1018 LKIQ01000000