Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	1,196,508	C→A	S338Y (TCT→TAT)	ftsZ →	Cell division protein FtsZ

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,196,508	0	C	A	100.0%	166.3 / NA	57	S338Y (TCT→TAT)	ftsZ	Cell division protein FtsZ
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (24/33);  total (24/33)

CGGTACAGTTATTAATCCTGAATTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTCTAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGATATTCCTAGCTTCATTAGAAATAGAGA  >  USA300TCH1516_ALE/1196377‑1196637                                                                                                                                    |                                                                                                                                  cGGTACAGTTATTAATCCTGAATTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAg                                                                                                                                >  1:545629/1‑135 (MQ=255)   atACAGTTATTAATCCTGAAGTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCa                                                                                                                              <  2:272186/134‑1 (MQ=255)     aCAGTTATTAATCCTGAATTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAAt                                                                                                                            >  1:434477/1‑135 (MQ=255)         ttattaATCCTGAATTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCaa                                                                                                                        >  1:549999/1‑135 (MQ=255)         ttattaATCCTGAATTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCaa                                                                                                                        >  1:322935/1‑135 (MQ=255)         ttattaATCCTGAATTACAAGATGAGATTATTATAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAAGGCaa                                                                                                                        >  1:26640/1‑135 (MQ=255)         ttattaATCCTGAATTACAAGATAAGATTGATGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACATATAGCAATGCaa                                                                                                                        >  1:70128/1‑135 (MQ=255)            ttaTTCCTGAATTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACCAGCGTCTACACTTATAGCAATGCAACtt                                                                                                                     >  1:400247/1‑135 (MQ=255)            ttaATCCTGAATTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACtt                                                                                                                     >  2:32232/1‑135 (MQ=255)            ttaATCCTGAATTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACtt                                                                                                                     >  1:547748/1‑135 (MQ=255)                tCCTGAATTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAAAACTTATAGCAATGCAAATTCTaa                                                                                                                 >  2:532292/1‑135 (MQ=255)                  cTGCATTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAg                                                                                                               >  1:46227/1‑135 (MQ=255)                  cTGAATTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTCGCACTGGATGCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAg                                                                                                               <  2:111644/135‑1 (MQ=255)                  cTGAATTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAg                                                                                                               <  2:538503/135‑1 (MQ=255)                  cTGAATTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACGTCTAAAg                                                                                                               >  1:285748/1‑135 (MQ=255)                            aGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCAtt                                                                                                     <  1:116115/135‑1 (MQ=255)                              aTGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCa                                                                                                   >  1:240961/1‑135 (MQ=255)                              aTGAGATTGTTGTAACAGTTATTGCAACTAGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCa                                                                                                   >  1:112126/1‑135 (MQ=255)                                 agaTTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGACTCATTCAcct                                                                                                >  1:88224/1‑133 (MQ=255)                                             tcgTTATTGCAAGTGGTTTTGATCACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGTGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCACTCACTTCAAATTCATCaa                                                                                    <  2:273003/133‑1 (MQ=255)                                             cAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAACTTCACCaa                                                                                    <  2:551211/135‑1 (MQ=255)                                             cAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCaa                                                                                    <  1:49006/135‑1 (MQ=255)                                               gTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTTACTTCAAATTCATCAAAt                                                                                  <  1:350610/135‑1 (MQ=255)                                                    tGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGcaca                                                                             >  1:335193/1‑135 (MQ=255)                                                       caCTGGTTTTGATAACAAACTAACAGCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTTTAAAGATGAATCATTCACTTCAAATTCATTAAATGCCCAAGc                                                                          <  1:458824/134‑1 (MQ=255)                                                       aaCTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGc                                                                          <  1:624912/135‑1 (MQ=255)                                                          tGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAAc                                                                       <  1:255393/135‑1 (MQ=255)                                                          tGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAAc                                                                       >  1:389805/1‑135 (MQ=255)                                                             ttttGATGACAAACCAACTTCCCCTTGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCCATCCAACTTCTAAAGTTTAATCATTCACTTCACATTCATCAAATGCACAAGTAACTGa                                                                    <  2:544774/135‑1 (MQ=255)                                                             ttttGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTTATCAAATGCACAAGCAACTGa                                                                    <  1:18044/135‑1 (MQ=255)                                                             ttttGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGa                                                                    <  1:406793/135‑1 (MQ=255)                                                             tttgGATGACAAACCACCATCACATGGTCGTAAATCTGGTAGCACTGGAATCGGAACAAGCGTAAATACTTATAGCAATGCCACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGa                                                                    <  2:382747/135‑1 (MQ=255)                                                                 gatgcCAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAAAAAGCGAAAAAACGTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAgt                                                                >  1:199184/1‑135 (MQ=255)                                                                 gatgaCAAAGCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAGCAAGCGTAAATACTTATAGGAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGAAAATGATAgg                                                                >  2:15092/1‑134 (MQ=255)                                                                   tgaCAAACCAACATCACATGGTCATAAATCTGGGAGCACTGGATTAGGCCTAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAgtgt                                                              >  1:409720/1‑135 (MQ=255)                                                                    gaCAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGACTCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTa                                                             <  1:392265/135‑1 (MQ=255)                                                                    gaCAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTa                                                             <  2:663130/135‑1 (MQ=255)                                                                    gaCAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTa                                                             <  2:583715/135‑1 (MQ=255)                                                                    gaCAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTa                                                             <  2:468349/135‑1 (MQ=255)                                                                      cAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAg                                                           <  1:163557/135‑1 (MQ=255)                                                                          ccAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGaa                                                       <  1:645841/135‑1 (MQ=255)                                                                          ccAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGaa                                                       <  1:646181/135‑1 (MQ=255)                                                                          ccAACATCACATGGTCGTAAATCTGCGAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATTAATCATTCACTTCAAATTCATCAAATGCATAAGCAACTGATAGTGTAAGTGaa                                                       <  1:352636/135‑1 (MQ=255)                                                                             aCATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGAGAAAGa                                                    <  1:34676/135‑1 (MQ=255)                                                                                     tGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATAc                                            <  2:564007/135‑1 (MQ=255)                                                                                                  ggTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAgat                               <  1:599396/135‑1 (MQ=255)                                                                                                   gTAGGACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAgatg                              <  1:399356/135‑1 (MQ=255)                                                                                                   gTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAgatg                              <  1:213495/135‑1 (MQ=255)                                                                                                   gTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAgatg                              <  1:53099/135‑1 (MQ=255)                                                                                                    gaGCACTGGATTCTGAACAAGCGTAAATACTGAGAGCAATGCAACTTCTAAAGATTAAACATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAgatga                             <  2:123358/134‑1 (MQ=255)                                                                                                          tGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGATATTcc                       >  2:531790/1‑135 (MQ=255)                                                                                                          tGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGATATTcc                       >  1:197820/1‑135 (MQ=255)                                                                                                          tGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGATATTcc                       >  1:230464/1‑135 (MQ=255)                                                                                                           ggATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAAATACTATTCCt                      >  2:78561/1‑135 (MQ=255)                                                                                                                cGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTTTAAGTGAAAGAACACATACAACTAAATAATATTATATTCCTAGCtt                 <  1:15092/135‑1 (MQ=255)                                                                                                                cGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGATATTCCTAGCtt                 <  2:507044/135‑1 (MQ=255)                                                                                                                               tACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTATTGATGTTGTTATTTCTTGCTTCATTAGAAATAgaga  <  1:2015/135‑1 (MQ=255)                                                                                                                                    |                                                                                                                                  CGGTACAGTTATTAATCCTGAATTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTCTAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGATATTCCTAGCTTCATTAGAAATAGAGA  >  USA300TCH1516_ALE/1196377‑1196637

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑