Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,704,711	G→T	intergenic (+35/‑238)	blr → / → cnu	beta‑lactam resistance protein/H‑NS‑ and StpA‑binding protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,704,711	0	G	T	100.0%	214.0 / NA	60	intergenic (+35/‑238)	blr/cnu	beta‑lactam resistance protein/H‑NS‑ and StpA‑binding protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base T (27/33);  total (27/33)

GTTGGATCGTTCTTGTCGTTTCAGTCATTCTTCTTGGCGTGGCGAGTCACATTGACAACTATCAGCCACCTGAACAGAGTGCTTCGGTACAACACAAGTAAGCTCTGCACTTGTGGAGCGACATGCTGCCCGTCCGGGTGCATGTTTTCACTTGTCGGATATTAAACCAGGAATTTATTATCTTGTTCGATGTTGTTGGTGATTGTCAGGGATAGTAAAGCGCGTTACTCTTTTCAGAGCAGTTTTTCATCCCTGAATATTTGCCATCAGCG  >  NC_000913/1704576‑1704847                                                                                                                                        |                                                                                                                                         gTTGGATCGTTCTTGTCGTTTCAGTCATTCTTCTTGGCGTGGCGAGTCACATTGACAACTATCAGCCACCTGAACAGAGTGCTTCGGTACAACACAAGTAAGCTCTGCACTTGTGGAGCGACATGCTGCCCGTCCTGGTg                                                                                                                                      >  2:101087/1‑140 (MQ=255) gTTGGATCGTTCTTGTCGTTTCAGTCATTCTTCTTGGCGTGGCGAGTCACATTGACAACTATCAGCCACCTGAACAGAGTGCTTCGGTACAACACAAGTAAGCTCTGCACTTGTGGAGCGACATGCTGCCCGTCCTGGTg                                                                                                                                      <  1:199979/140‑1 (MQ=255)      aTCGTTCTTGTCGTTTCAGTCATTCTTCTTGGCGTGGCGAGTCACATTGACAACTATCAGCCACCTGAACAGAGTGCTTCGGTACAACACAAGTAAGCTCTGCACTTGTGGAGCGACATGCTGCCCGTCCTGGTGCATGt                                                                                                                                 >  1:493326/1‑140 (MQ=255)         gTTCTTGTCGTTTCAGTCATTCTTCTTGGCGTGGCGAGTCACATTGACAACTATCAGCCTCCTGAACAGAGTGCTTCGGTACAACACAAGTAAGCTCTGCACTTGTGGAGCGACATGCTGCCCGTCCTGGTGCATGtttt                                                                                                                              <  2:706701/140‑1 (MQ=255)         gTTCTTGTCGTTTCAGTCATTCTTCTTGGCGTGGCGAGTCACATTGACAACTATCAGCCACCTGAACAGAGTGCTTCGGTACAACACAAGTAAGCTCTGCACTTGTGGAGCGACATGCTGCCCGTCCTGGTGCATGtttt                                                                                                                              <  1:336144/140‑1 (MQ=255)            cTTGTCGTTTCAGTCATTCTTCTTGGCGTGGCGCATCACATTGACAACTATCAGCCACCTGAACAGAGTACTTCGGTACAACACAAGTAAGCTCTGCACTTGTGGAGCGACATGCTGCCCGTCCTGGTGCATGTTTTCAc                                                                                                                           >  2:546791/1‑140 (MQ=255)                  gTTTCAGTCATTCTTCTTGGCGTGGCGAGTCACATTGACAACTATCAGCCACCTGAACAGAGTGCTTCGGTACAACACAAGTAAGCTCTGCACTTGTGGAGCGACATGCTGCCCGTCCTGGTGCATGTTTTCACTTGTCg                                                                                                                     <  1:111627/140‑1 (MQ=255)                  gTTTCAGTCATTCTTCTTGGCGTGGCGAGTCACATTGACAACTATCAGCCACCTGAACAGAGTGCTTCGGTACAACACAAGTAAGCTCTGCACTTGTGGAGCGACATGCTGCCCGTCCTGGTGCATGTTTTCACTTGTCg                                                                                                                     <  1:653422/140‑1 (MQ=255)                  gTTTCAGTCATTCTTCTTGGCGTGGCGAGTCACATTGACAACTATCAGCCACCTGAACAGAGTGCTTCGGTACAACACAAGTAAGCTCTGCACTTGTGGAGCGACATGCTGCCCGTCCTGGTGCATGTTTTCACTTGTCg                                                                                                                     <  2:675713/140‑1 (MQ=255)                               ttcttGGCGTGGCGAGTCACATTGACAACTATCAGCCACCTGAACAGAGTGCTTCGGTACAACACAAGTAAGCTCTGCACTTGTGGAGCGACATGCTGCCCGTCCTGGTGCATGTTTTCACTTGTCGGATATTAAACCAg                                                                                                        <  1:647174/140‑1 (MQ=255)                                 cttGGCGTGGCGAGTCACATTGACAACTATCAGCCACCTGAACAGAGTGCTTCGGTACAACACAAGTAAGCTCTGCACTTGTGGAGCGACATGCTGCCCGTCCTGGTGCATGTTTTCACTTGTCGGATATTAAACCAGGa                                                                                                      >  1:286015/1‑140 (MQ=255)                                 cttGGCGTGGCGAGTCACATTGACAACTATCAGCCACCTGAACAGAGTGCTTCGGTACAACACAAGTAAGCTCTGCACTTGTGGAGCGACATGCTGCCCGTCCTGGTGCATGTTTTCACTTGTCGGATATTAAACCAGGa                                                                                                      >  2:614799/1‑140 (MQ=255)                                 cttGGCGTGGCGAGTCACATTGACAACTATCAGCCACCTGAACAGAGTGCTTCGGTACAACACAAGTAAGCTCTGCACTTGTGGAGCGACATGCTGCCCGTCCTGGTGCATGTTTTCACTTGTCGGATATTAAACCAGGa                                                                                                      <  2:506674/140‑1 (MQ=255)                                      cgtggcgAGTCACATTGACAACTATCAGCCACCTGAACAGAGTGCTTCGGTACAACACAAGTAAGCTCTGCACTTGTGGAGCGACATGCTGCCCGTCCTGGTGCATGTTTTCACTTGTCGGATATTAAACCAGGAATtta                                                                                                 <  1:630900/140‑1 (MQ=255)                                      cgtggcgAGTCACATTGACAACTATCAGCCACCTGAACAGAGTGCTTCGGTACAACACAAGTAAGCTCTGCACTTGTGGAGCGACATGCTGCCCGTCCTGGTGCATGTTTTCACTTGTCGGATATTAAACCAGGAATtta                                                                                                 <  1:582088/140‑1 (MQ=255)                                          gcgAGTCACATTGACAACTATCAGCCACCTGAACAGAGTGCTTCGGTACAACACAAGTAAGCTCTGCACTTGTGGAGCGACATGCTGCCCGTCCTGGTGCATGTTTTCACTTGTCGGATATTAAACCAGGAATTtattat                                                                                             <  1:584351/140‑1 (MQ=255)                                                    ttGACAACTATCAGCCACCTGAACAGAGTGCTTCGGTACAACACAAGTAAGCTCTGCACTTGTGGAGCGACATGCTGCCCGTCCTGGTGCATGTTTTCACTTGTCGGATATTAAACCAGGAATTTATTATCTTGTTCGAt                                                                                   >  2:434259/1‑140 (MQ=255)                                                     tGACAACTATCAGCCACCTGAACAGAGTGCTTCGGTACAACACAAGTAAGCTCTGCACTTGTGGAGCGACATGCTGCCCGTCCTGGTGCATGTTTTCACTTGTCGGATATTAAACCAGGAATTTATTATCTTGTTCGAtg                                                                                  <  1:233577/140‑1 (MQ=255)                                                       aCAACTATCAGCCACCTGAACAGAGTGCTTCGGTACAACACAAGTAAGCTCTGCACTTGTGGAGCGACATGCTGCCCGTCCTGGTGCATGTTTTCACTTGTCGGATATTAAACCAGGAATTTATTATCTTGTTCGAtgtt                                                                                >  2:205895/1‑140 (MQ=255)                                                            tATCAGCCACCTGAACAGAGTGCTTCGGTACAACACAAGTAAGCTCTGCACTTGTGGAGCGACATGCTGCCCGTCCTGGTGCATGTTTTCACTTGTCGGATATTAAACCAGGAATTTATTATCTTGTTCGATGTTGTTgg                                                                           <  2:582902/140‑1 (MQ=255)                                                             aTCAGCCACCTGAACAGAGTGCTTCGGTACAACACAAGTAAGCTCTGCACTTGTGGAGCGACATGCTGCCCGTCCTGGTGCATGTTTTCACTTGTCGGATATTAAACCAGGAATTTATTATCTTGTTCGATGTTGTTGGt                                                                          <  1:434259/140‑1 (MQ=255)                                                             aTCAGCCACCTGAACAGAGTGCTTCGGTACAACACAAGTAAGCTCTGCACTTGTGGAGCGACATGCTGCCCGTCCTGGTGCATGTTTTCACTTGTCGGATATTAAACCAGGAATTTATTATCTTGTTCGATGTTGTTGGt                                                                          >  1:403974/1‑140 (MQ=255)                                                             aTCAGCCACCTGAACAGAGTGCTTCGGTACAACACAAGTAAGCTCTGCACTTGTGGAGCGACATGCTGCCCGTCCTGGTGCATGTTTTCACTTGTCGGATATTAAACCAGGAATTTATTATCTTGTTCGATGTTGTTGGt                                                                          <  1:155174/140‑1 (MQ=255)                                                                   cACCTGAACAGAGTGCTTCGGTACAACACAAGTAAGCTCTGCACTTGTGGAGCGACATGCTGCCCGTCCTGGTGCATGTTTTCACTTGTCGGATATTAAACCAGGAATTTATTATCTTGTTCGATGTTGTTGGTGATTGt                                                                    <  2:572809/140‑1 (MQ=255)                                                                   cACCTGAACAGAGTGCTTCGGTACAACACAAGTAAGCTCTGCACTTGTGGAGCGACATGCTGCCCGTCCTGGTGCATGTTTTCACTTGTCGGATATTAAACCAGGAATTTATTATCTTGTTCGATGTTGTTGGTGATTGt                                                                    <  2:408477/140‑1 (MQ=255)                                                                    tccTGAACAGAGTGCTTCGGTACAACACAAGTAAGCTCTGCACTTGTGGAGCGACATGCTGCCCGTCCTGGTGCATGTTTTCTCTTGTCGGATATTAAACCAGGAATTTATTATCTTGTTCGATGTTGTTGGTGATTGTc                                                                   <  2:277112/139‑1 (MQ=255)                                                                    aCCTGAACAGAGTGCTTCGGTACAACACAAGTAAGCTCTGCACTTGTGGAGCGACATGCTGCCCGTCCTGGTGCATGTTTTCACTTGTCGGATATTAAACCAGGAATTTATTATCTTGTTCGATGTTGTTGGTGATTGTc                                                                   <  1:508448/140‑1 (MQ=255)                                                                    aCCTGAACAGAGTGCTTCGGTACAACACAAGTAAGCTCTGCACTTGTGGAGCGACATGCTGCCCGTCCTGGTGCATGTTTTCACTTGTCGGATATTAAACCAGGAATTTATTATCTTGTTCGATGTTGTTGGTGATTGTc                                                                   <  2:286015/140‑1 (MQ=255)                                                                     ccTGAACAGAGTGCTTCGGTACAACACAAGTAAGCTCTGCACTTGTGGAGCGACATGCTGCCCGTCCTGGTGCATGTTTTCACTTGTCGGATATTAAACCAGGAATTTATTATCTTGTTCGATGTTGTTGGTGATTGTc                                                                   <  1:602650/139‑1 (MQ=255)                                                                     ccTGAACAGAGTGCTTCGGTACAACACAAGTAAGCTCTGCACTTGTGGAGCGACATGCTGCCCGTCCTGGTGCATGTTTTCACTTGTCGGATATTAAACCAGGAATTTATTATCTTGTTCGATGTTGTTGGTGATTGTc                                                                   >  2:602650/1‑139 (MQ=255)                                                                      cTGAACAGAGTGCTTCGGTACAACACAAGTAAGCTCTGCACTTGTGGAGCGACATGCTGCCCGTCCTGGTGCATGTTTTCACTTGTCGGATATTAAACCAGGAATTTATTATCTTGTTCGATGTTGTTGGTGATTGTCAg                                                                 >  2:103651/1‑140 (MQ=255)                                                                               gTGCTTCGGTACAACACAAGTAAGCTCTGCACTTGTGGAGCGACATGCTGCCCGTCCTGGTGCATGTTTTCACTTGTCGGATATTAAACCAGGAATTTATTATCTTGTTCGATGTTGTTGGTGATTGTCAGGGATAGTaa                                                        >  1:396444/1‑140 (MQ=255)                                                                                tGCTTCGGTACAACACAAGTAAGCTCTGCACTTGTGGAGCGACATGCTGCCCGTCCTGGTGCATGTTTTCACTTGTCGGATATTAAACCAGGAATTTATTATCTTGTTCGATGTTGTTGGTGATTGTCAGGGATAGTaaa                                                       <  1:205895/140‑1 (MQ=255)                                                                                tGCTTCGGTACAACACAAGTAAGCTCTGCACTTGTGGAGCGACATGCTGCCCGTCCTGGTGCATGTTTTCACTTGTCGGATATTAAACCAGGAATTTATTATCTTGTTCGATGTTGTTGGTGATTGTCAGGGATAGTaaa                                                       >  2:331432/1‑140 (MQ=255)                                                                                tGCTTCGGTACAACACAAGTAAGCTCTGCACTTGTGGAGCGACATGCTGCCCGTCCTGGTGCATGTTTTCACTTGTCGGATATTAAACCAGGAATTTATTATCTTGTTCGATGTTGTTGGTGATTGTCAGGGATAGTaaa                                                       <  2:49650/140‑1 (MQ=255)                                                                                tGCTTCGGTACAACACAAGTAAGCTCTGCACTTGTGGAGCGACATGCTGCCCGTCCTGGTGCATGTTTTCACTTGTCGGATATTAAACCAGGAATTTATTATCTTGTCCGATGTTGTTGGTGATTGTCAGGGATAGTaaa                                                       <  1:436249/140‑1 (MQ=255)                                                                                   ttCGGTACAACACAAGTAAGCTCTGCACTTGTGGAGCGACATGCTGCCCGTCCTGGTGCATGTTTTCACTTGTCGGATATTAAACCAGGAATTTATTATCTTGTTCGATGTTGTTGGTGATTGTCAGGGATAGTAAAgcg                                                    >  1:707590/1‑140 (MQ=255)                                                                                        tACAACACAAGTAAGCTCTGCACTTGTGGAGCGACATGCTGCCCGTCCTGGTGCATGTTTTCACTTGTCGGATATTAAACCAGGAATTTATTATCTTGTTCGATGTTGTTGGTGATTGTCAGGGATAGTAAAGCGCGTTa                                               <  2:567331/140‑1 (MQ=255)                                                                                             cacaAGTAAGCTCTGCACTTGTGGAGCGACATGCTGCCCGTCCTGGTGCATGTTTTCACTTGTCGGATATTAAACCAGGATTTTATTATCTTGTTCAATGTTGTTGGTGATTGTCAGGGATAGTAAAGCGCGTTACTCtt                                          >  2:80636/1‑140 (MQ=255)                                                                                                       ctctGCACTTGTGGAGCGACATGCTGCCCGTCCTGGTGCATGTTTTCACTTGTCGGATATTAAACCAGGAATTTATTATCTTGTTCGATGTTGTTGGTGATTGTCAGGGATAGTAAAGCGCGTTACTCTTTTCAGAGCAg                                >  1:32499/1‑140 (MQ=255)                                                                                                       ctctGCACTTGTGGAGCGACATGCTGCCCGTCCTGGTGCATGTTTTCACTTGTCGGATATTAAACCAGGAATTTATTATCTTGTTCGATGTTGTTGGTGATTGTCAGGGATAGTAAAGCGCGTTACTCTTTTCAGAGCAg                                >  2:585463/1‑140 (MQ=255)                                                                                                            cACTTGTGGAGCGACATGCTGCCCGTCCTGGTGCATGTTTTCACTTGTCGGATATTAAACCAGGAATTTATTATCTTGTTCGATGTTGTTGGTGATTGTCAGGGATAGTAAAGCGCGTTACTCTTTTCAGAGCAGttttt                           >  2:85630/1‑140 (MQ=255)                                                                                                            cACTTGTGGAGCGACATGCTGCCCGTCCTGGTGCATGTTTTCACTTGTCGGATATTAAACCAGGAATTTATTATCTTGTTCGATGTTGTTGGTGATTGTCAGGGATAGTAAAGCGCGTTACTCTTTTCAGAGCAGttttt                           <  2:372679/140‑1 (MQ=255)                                                                                                            cACTTGTGGAGCGACATGCTGCCCGTCCTGGTGCATGTTTTCACTTGTCGGATATTAAACCAGGAATTTATTATCTTGTTCGATGTTGTTGGTGATTGTCAGGGATAGTAAAGCGCGTTACTCTTTTCAGAGCAGttttt                           >  1:690780/1‑140 (MQ=255)                                                                                                            cACTTGTGGAGCGACATGCTGCCCGTCCTGGTGCATGTTTTCACTTGTCGGATATTAAACCAGGAATTTATTATCTTGTTCGATGTTGTTGGTGATTGTCAGGGATAGTAAAGCGCGTTACTCTTTTCAGAGCAGttttt                           >  2:479485/1‑140 (MQ=255)                                                                                                              cTTGTGGAGCGACATGCTGCCCGTCCTGGTGCATGTTTTCACTTGTCGGATATTAAACCAGGAATTTATTATCTTGTTCGATGTTGTTGGTGATTGTCAGGGATAGTAAAGCGCGTTACTCTTTTCAGAGCAGTTTTTCa                         <  2:513863/140‑1 (MQ=255)                                                                                                              cTTGTGGAGCGACATGCTGCCCGTCCTGGTGCATGTTTTCACTTGTCGGATATTAAACCAGGAATTTATTATCTTGTTCGATGTTGTTGGTGATTGTCAGGGATAGTAAAGCGCGTTACTCTTTTCAGAGCAGTTTTTCa                         <  2:70201/140‑1 (MQ=255)                                                                                                                 gtgGAGCGACATGCTGCCCGTCCTGGTGCATGTTTTCACTTGTCGGATATTAAACCAGGAATTTATTATCTTGTTCGATGTTGTTGGTGATTGTCAGGGATAGTAAAGCGCGTTACTCTTTTCAGAGCAGTTTTTCATcc                      >  1:272300/1‑140 (MQ=255)                                                                                                                 gtgGAGCGACATGCTGCCCGTCCTGGTGCATGTTTTCACTTGTCGGATATTAAACCAGGAATTTATTATCTTGTTCGATGTTGTTGGTGATTGTCAGGGATAGTAAAGCGCGTTACTCTTTTCAGAGCAGTTTTTCATcc                      >  2:300789/1‑140 (MQ=255)                                                                                                                 gtgGAGCGACATGCTGCCCGTCCTGGTGCATGTTTTCACTTGTCGGATATTAAACCAGGAATTTATTATCTTGTTCGATGTTGTTGGTGATTGTCAGGGATAGTAAAGCGCGTTACTCTTTTCAGAGCAGTTTTTCATcc                      <  1:103651/140‑1 (MQ=255)                                                                                                                    gAGCGACATGCTGCCCGTCCTGGTGCATGTTTTCACTTGTCGGATATTAAACCAGGAATTTATTATCTTGTTCGATGTTGTTGGTGATTGTCAGGGATAGTAAAGCGCGTTACTCTTTTCAGAGCAGTTTTTCATCCCTg                   >  2:336293/1‑140 (MQ=255)                                                                                                                    gAGCGACATGCTGCCCGTCCTGGTGCATGTTTTCACTTGTCGGATATTAAACCAGGAATTTATTATCTTGTTCGATGTTGTTGGTGATTGTCAGGGATAGTAAAGCGCGTTACTCTTTTCAGAGCAGTTTTTCATCCCTg                   >  1:726079/1‑140 (MQ=255)                                                                                                                         aCATGCTGCCCGTCCTGGTGCATGTTTTCACTTGTCGGATATTAAACCAGGAATTTATTATCTTGTTCGATGTTGTTGGTGATTGTCAGGGATAGTAAAGCGCGTTACTCTTTTCAGAGCAGTTTTTCa                         <  1:174356/129‑1 (MQ=255)                                                                                                                         aCATGCTGCCCGTCCTGGTGCATGTTTTCACTTGTCGGATATTAAACCAGGAATTTATTATCTTGTTCGATGTTGTTGGTGATTGTCAGGGATAGTAAAGCGCGTTACTCTTTTCAGAGCAGTTTTTCa                         >  2:174356/1‑129 (MQ=255)                                                                                                                         aCATGCTGCCCGTCCTGGTGCATGTTTTCACTTGTCGGATATTAAACCAGGAATTTATTATCTTGTTCGATGTTGTTGGTGATTGTCAGGGATAGTAAAGCGCGTTACTCTTTTCAGAGCAGTTTTTCATCCCTGAatat              >  1:516075/1‑140 (MQ=255)                                                                                                                         aCATGCTGCCCGTCCTGGTGCATGTTTTCACTTGTCGGATATTAAACCAGGAATTTATTATCTTGTTCGATGTTGTTGGTGATTGTCAGGGATAGTAAAGCGCGTTACTCTTTTCAGAGCAGTTTTTCATCCCTGAatat              >  1:350813/1‑140 (MQ=255)                                                                                                                            tgctgcCCGTCCTGGTGCATGTTTTCACTTGTCGGATATTAAACCAGGAATTTATTATCTTGTTCGATGTTGTTGGTGATTGTCAGGGATAGTAAAGCGCGTTACTCTTTTCAGAGCAGTTTTTCATCCCTGAATATTTg           >  2:10422/1‑140 (MQ=255)                                                                                                                            tgctgcCCGTCCTGGTGCATGTTTTCACTTGTCGGATATTAAACCAGGAATTTATTATCTTGTTCGATGTTGTTGGTGATTGTCAGGGATAGTAAAGCGCGTTACTCTTTTCAGAGCAGTTTTTCATCCCTGAATATTTg           >  1:465588/1‑140 (MQ=255)                                                                                                                                   cGTCCTGGTGCATGTTTTCACTTGTCGGATATTAAACCAGGAATTTATTATCTTGTTCGATGTTGTTGGTGATTGTCAGGGATAGTAAAGCGCGTTACTCTTTTCAGAGCAGTTTTTCATCCCTGAATATTTGCCATCAg    <  2:396444/140‑1 (MQ=255)                                                                                                                                    gTCCTGGTGCATGTTTTCACTTGTCGGATATTAAACCAGGAATTTATTATCTTGTTCGATGTTGTTGGTGATTGTCAGGGATAGTAAAGCGCGTTACTCTTTTCAGAGCAGTTTTTCATCCCTGAATATTTGCCATCAgc   <  2:707590/140‑1 (MQ=255)                                                                                                                                     tCCTGGTGCATGTTTTCACTTGTCGGATATTAAACCAGGAATTTATTATCTTGTTCGATGTTGTTGGTGATTGTCAGGGATAGTAAAGCGCGTTACTCTTTTCAGAGCAGTTTTTCATCCCTGAATATTTGCCATCAgcg  <  2:726079/140‑1 (MQ=255)                                                                                                                                        |                                                                                                                                         GTTGGATCGTTCTTGTCGTTTCAGTCATTCTTCTTGGCGTGGCGAGTCACATTGACAACTATCAGCCACCTGAACAGAGTGCTTCGGTACAACACAAGTAAGCTCTGCACTTGTGGAGCGACATGCTGCCCGTCCGGGTGCATGTTTTCACTTGTCGGATATTAAACCAGGAATTTATTATCTTGTTCGATGTTGTTGGTGATTGTCAGGGATAGTAAAGCGCGTTACTCTTTTCAGAGCAGTTTTTCATCCCTGAATATTTGCCATCAGCG  >  NC_000913/1704576‑1704847

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑