Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	1,185,357	C→T	E183K (GAG→AAG)	phoP ←	two‑component system response regulator PhoP

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,185,357	0	C	T	100.0%	173.2 / NA	43	E183K (GAG→AAG)	phoP	two‑component system response regulator PhoP
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (22/21);  total (22/21)

TAATCACTTCTTGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATGGTATGGCTTTCCCGCAGCTCCGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGTATCAACGTTTCCATAATAGTG  >  NZ_CP009273/1185273‑1185439                                                                                     |                                                                                   tAATCACTTCTTGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATGGTATGGCTTTCCCGCAGCTTCGCAt                                                                               <  2:1074542/90‑1 (MQ=255)  aaTCACTTCTTGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATGGTATGGCTTTCCCGCAGCTTCGCATc                                                                              >  2:1324513/1‑90 (MQ=255)     cACTTCTTGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATGGTATGGCTTTCCCGCAGCTTCGCATCCgg                                                                           <  2:1211347/90‑1 (MQ=255)     cACTTCTTGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATGGTATGGCTTTCCCGCAGCTTCGCATCCgg                                                                           >  1:327359/1‑90 (MQ=255)     cACTTCTTGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATGGTATGGCTTTCCCGCAGCTTCGCATCCgg                                                                           >  2:697621/1‑90 (MQ=255)       cttcttGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATGGTATGGCTTTCCCGCAGCTTCGCATCCGGAt                                                                         <  2:624113/90‑1 (MQ=255)       cttcttGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATGGTATGGCTTTCCCGCAGCTTCGCATCCGGAt                                                                         >  2:165523/1‑90 (MQ=255)       cttcttGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATGGTATGGCTTTCCCGCAGCTTCGCATCCGGAt                                                                         >  1:643213/1‑90 (MQ=255)       cttcttGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATGGTATGGCTTTCCCGCAGCTTCGCATCCGGAt                                                                         >  2:939627/1‑90 (MQ=255)       cttcttGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATGGTATGGCTTTCCCGCAGCTTCGCATCCGGAt                                                                         >  1:619786/1‑90 (MQ=255)                        gCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATGGTATGGCTTTCCCGCAGCTTCGCATCCGGATAGAGTTGGAGCATTAAc                                                        >  1:1199871/1‑90 (MQ=255)                        gCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATGGTATGGCTTTCCCGCAGCTTCGCATCCGGATAGAGTTGGAGCATTAAc                                                        >  2:1136897/1‑90 (MQ=255)                        gCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATGGTATGGCTTTCCCGCAGCTTCGCATCCGGATAGAGTTGGAGCATTAAc                                                        >  2:1076028/1‑90 (MQ=255)                        gCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATGGTATGGCTTTCCCGCAGCTTCGCATCCGGATAGAGTTGGAGCATTAAc                                                        >  1:387282/1‑90 (MQ=255)                          cTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATGGTATGGCTTTCCCGCAGCTTCGCATCCGGATAGAGTTGGAGCATTAACGa                                                      <  2:1056873/90‑1 (MQ=255)                               tttttttGCGCAGACGTCCCATCAGTACATCAATGGTATGGCTTTCCCGCAGCTTCGCATCCGGATAGAGTTGGAGCATTAACGAATCtt                                                 <  2:391830/90‑1 (MQ=255)                               tttttttGCGCAGACGTCCCATCAGTACATCAATGGTATGGCTTTCCCGCAGCTTCGCATCCGGATAGAGTTGGAGCATTAACGAATCtt                                                 <  1:402337/90‑1 (MQ=255)                                      gcgcAGACGTCCCATCAGTACATCAATGGTATGGCTTTCCCGCAGCTTCGCATCCGGATAGAGATGGAGCATTAACGAATCTTTGCTGAc                                          <  1:1042126/90‑1 (MQ=255)                                           gACGTCCCATCAGTACATCAATGGTATGGCTTTCCCGCAGCTTCGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCACtt                                     <  1:939627/90‑1 (MQ=255)                                               tCCCATCAGTACATCAATGGTATGGCTTTCCCGCAGCTTCGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCACTTTGcc                                 <  2:40378/90‑1 (MQ=255)                                                     cAGTACATCAATGGTATGGCTTTCCCGCAGCTTCGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCACTTTGCCattatt                           >  1:313018/1‑90 (MQ=255)                                                       gTACATCAATGGTATGGCTTTCCCGCAGCTTCGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGc                         >  2:89222/1‑90 (MQ=255)                                                         aCATCAATGGTATGGCTTTCCCGCAGCTTCGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGt                       >  1:924370/1‑90 (MQ=255)                                                         aCATCAATGGTATGGCTTTCCCGCAGCTTCGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGt                       >  1:71327/1‑90 (MQ=255)                                                            tCAATGGTATGGCTTTCCCGCAGCTTCGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGTATc                    >  2:1115377/1‑90 (MQ=255)                                                             cAATGGTATGGCTTTCCCGCAGCTTCGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGTATCa                   <  2:1164685/90‑1 (MQ=255)                                                                tGGTATGGCTTTCCCGCAGCTTCGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGTATCAACg                <  2:327359/90‑1 (MQ=255)                                                                 ggTATGGCTTTCCCGCAGCTTCGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGTATCAACGt               >  2:31936/1‑90 (MQ=255)                                                                 ggTATGGCTTTCCCGCAGCTTCGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGTATCAACGt               >  1:627485/1‑90 (MQ=255)                                                                 ggTATGGCTTTCCCGCAGCTTCGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGTATCAACGt               >  1:930522/1‑90 (MQ=255)                                                                 ggTATGGCTTTCCCGCAGCTTCGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGTATCAACGt               >  1:805060/1‑90 (MQ=255)                                                                  gTATGGCTTTCCCGCAGCTTCGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGTATCAACGtt              <  2:619786/90‑1 (MQ=255)                                                                  gTATGGCTTTCCCGCAGCTTCGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGTATCAACGtt              <  1:31936/90‑1 (MQ=255)                                                                  gTATGGCTTTCCCGCAGCTTCGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGTATCAACGtt              <  1:393318/90‑1 (MQ=255)                                                                  gTATGGCTTTCCCGCAGCTTCGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGTATCAACGtt              <  2:798263/90‑1 (MQ=255)                                                                  gTATGGCTTTCCCGCAGCTTCGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGTATCAACGtt              <  2:1099674/90‑1 (MQ=255)                                                                     tGGCTTTCCCGCAGCTTCGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGTATCAACGTTTcc           <  2:643213/90‑1 (MQ=255)                                                                     tGGCTTTCCCGCAGCTTCGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGTATCAACGTTTcc           <  2:805060/90‑1 (MQ=255)                                                                       gCTTTCCCGCAGCTTCGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGTATCAACGTTTCCat         >  2:160204/1‑90 (MQ=255)                                                                          ttCCCGCAGCTTCGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTg                                            <  1:945559/52‑1 (MQ=255)                                                                          ttCCCGCAGCTTCGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTg                                            >  2:945559/1‑52 (MQ=255)                                                                            cccGCAGCTTCGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGTATCAACGTTTCCATAATAg    <  2:1181129/90‑1 (MQ=255)                                                                              cGCAGCTTCGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGTATCAACGTTTCCATAATAgtg  <  2:149581/90‑1 (MQ=255)                                                                                     |                                                                                   TAATCACTTCTTGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATGGTATGGCTTTCCCGCAGCTCCGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGTATCAACGTTTCCATAATAGTG  >  NZ_CP009273/1185273‑1185439

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑