Table 1 Characteristics of the isolates sequenced in this study
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 |