Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	3,098,336	Δ1 bp	coding (545/1080 nt)	mltC →	membrane‑bound lytic murein transglycosylase MltC

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,098,335	0	C	.	100.0%	365.3 / NA	81	coding (544/1080 nt)	mltC	membrane‑bound lytic murein transglycosylase MltC
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base . (44/37);  total (44/37)

GCAACTTCGCGGATTATCTGCTGAAAAACCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTGCCGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCACGGAAATATGGCGTTGATGAGTCGCTGAT  >  NZ_CP009273/3098246‑3098420                                                                                          |                                                                                      gcaaCTTCGCGGATTATCTGCTGAAAAACCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTGc                                                                                       >  2:2595624/1‑90 (MQ=255)   aaCTTCGCGGATTATCTGCTGAAAAACCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTGcga                                                                                     <  1:659728/90‑3 (MQ=255)    aCTTCGCGGATTATCTGCTGAAAAACCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTGcgaa                                                                                    <  1:1125062/90‑4 (MQ=255)    aCTTCGCGGATTATCTGCTGAAAAACCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTGcgaa                                                                                    <  2:572564/90‑4 (MQ=255)    aCTTCGCGGATTATCTGCTGAAAAACCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTGcgaa                                                                                    <  1:1607450/90‑4 (MQ=255)     cTTCGCGGATTATCTGCTGAAAAACCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTGcgaac                                                                                   <  2:609537/90‑5 (MQ=255)     cTTCGCGGATTATCTGCTGAAAAACCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTGcgaac                                                                                   <  2:2353474/90‑5 (MQ=255)     cTTCGAGGATTATCTGCTGAAAAACCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTGcgaac                                                                                   <  1:2039952/90‑5 (MQ=255)       tCGCGGATTATCTGCTGAAAAACCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAacca                                                                                <  2:767323/90‑1 (MQ=255)         gcgGATTATCTGCTGAAAAACCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAaccacc                                                                              <  1:1038890/90‑1 (MQ=255)         gcgGATTATCTGCTGAAAAACCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAaccacc                                                                              <  2:107433/90‑1 (MQ=255)         gcgGATTATCTGCTGAAAAACCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAaccacc                                                                              <  2:1319398/90‑1 (MQ=255)         gcgGATTATCTGCTGAAAAACCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAaccacc                                                                              <  2:1413912/90‑1 (MQ=255)         gcgGATTATCTGCTGAAAAACCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAaccacc                                                                              <  1:2400218/90‑1 (MQ=255)         gcgGATTATCTGCTGAAAAACCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAaccacc                                                                              <  2:1879974/90‑1 (MQ=255)         gcgGATTATCTGCTGAAAAACCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAaccacc                                                                              <  1:1765006/90‑1 (MQ=255)                    gctgAAAAACCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGt                                                                   >  1:1642633/1‑90 (MQ=255)                    gctgAAAAACCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGt                                                                   <  1:531079/90‑1 (MQ=255)                      tgAAAAACCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTgc                                                                 <  2:2620924/90‑1 (MQ=255)                      tgAAAAACCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTgc                                                                 >  2:520667/1‑90 (MQ=255)                      tgAAAAACCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTgc                                                                 >  2:2719523/1‑90 (MQ=255)                       gAAAAACCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTg                                                                  >  1:821252/1‑88 (MQ=255)                       gAAAAACCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTg                                                                  <  2:821252/88‑1 (MQ=255)                        aaaaaCCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTgcgc                                                               <  2:2150481/90‑1 (MQ=255)                        aaaaaCCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTgcgc                                                               <  1:2659225/90‑1 (MQ=255)                        aaaaaCCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTgcgc                                                               <  1:1512832/90‑1 (MQ=255)                        aaaaaCCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTgcgc                                                               <  1:1593583/90‑1 (MQ=255)                         aaaaCCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGca                                                              <  1:267064/90‑1 (MQ=255)                            aCCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAaccacc                                                                              >  2:264328/1‑71 (MQ=255)                            aCCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAaccacc                                                                              <  1:264328/71‑1 (MQ=255)                              cGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAat                                                         >  1:2560373/1‑90 (MQ=255)                               gTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAata                                                        >  2:1628536/1‑90 (MQ=255)                                      gagCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGc                                                 >  2:171099/1‑90 (MQ=255)                                       agCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCa                                                <  2:2452669/90‑1 (MQ=255)                                        gCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCAt                                               >  2:2053765/1‑90 (MQ=255)                                        gCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCAt                                               <  1:1062637/90‑1 (MQ=255)                                        gCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCAt                                               <  1:1689555/90‑1 (MQ=255)                                        gCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCAt                                               <  1:1567372/90‑1 (MQ=255)                                           gcagcaACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGt                                            >  1:1703028/1‑90 (MQ=255)                                           gcagcaACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGt                                            <  2:2316176/90‑1 (MQ=255)                                                 aCGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCa                                      <  1:741542/90‑1 (MQ=255)                                                   gggCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAgg                                    >  1:2773453/1‑90 (MQ=255)                                                   gggCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAgg                                    >  1:1213609/1‑90 (MQ=255)                                                      cTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGt                                 >  2:2155538/1‑90 (MQ=255)                                                      cTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGt                                 >  2:1102143/1‑90 (MQ=255)                                                       tGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTc                                <  1:1102143/90‑1 (MQ=255)                                                       tGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTc                                <  2:2556141/90‑1 (MQ=255)                                                       tGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTc                                <  1:2513734/90‑1 (MQ=255)                                                        gCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACaaa                                                          >  2:295401/1‑63 (MQ=255)                                                        gCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACaaa                                                          <  1:295401/63‑1 (MQ=255)                                                        gCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCa                               >  1:413832/1‑90 (MQ=255)                                                        gCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCa                               >  1:1830318/1‑90 (MQ=255)                                                        gCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCa                               >  1:1932459/1‑90 (MQ=255)                                                        gCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCa                               >  2:1791796/1‑90 (MQ=255)                                                        gCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCa                               >  1:2413868/1‑90 (MQ=255)                                                        gCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCa                               >  1:531992/1‑90 (MQ=255)                                                         cGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCAc                              <  1:1246572/90‑1 (MQ=255)                                                         cGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCAc                              <  2:1314909/90‑1 (MQ=255)                                                         cGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCAc                              <  1:1235527/90‑1 (MQ=255)                                                              catcTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTgcgc                                                               <  1:1682655/52‑1 (MQ=255)                                                              catcTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTgcgc                                                               >  2:1682655/1‑52 (MQ=255)                                                                 cTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCACGGAAatat                      <  1:1156590/90‑1 (MQ=255)                                                                 cTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCACGGAAatat                      <  2:1978332/90‑1 (MQ=255)                                                                  tACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCACGGAAATATg                     >  2:1700821/1‑90 (MQ=255)                                                                  tACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCACGGAAATATg                     >  1:44946/1‑90 (MQ=255)                                                                    cAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCACGGAAATATGGc                   >  1:1447870/1‑90 (MQ=255)                                                                     aGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCACGGAAATATGGCg                  >  2:1076542/1‑90 (MQ=255)                                                                      gCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTgcgc                                                               >  2:1868543/1‑44 (MQ=255)                                                                      gCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTgcgc                                                               <  1:1868543/44‑1 (MQ=255)                                                                      gCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTc                                <  2:816267/75‑1 (MQ=255)                                                                      gCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTc                                >  1:816267/1‑75 (MQ=255)                                                                      gCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCACGGAAATATGGCGt                 >  2:914768/1‑90 (MQ=255)                                                                      gCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCACGGAAATATGGCGt                 >  1:576062/1‑90 (MQ=255)                                                                      gCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCACGGAAATATGGCGt                 >  1:2677273/1‑90 (MQ=255)                                                                        gTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTc                                           >  2:2458218/1‑62 (MQ=255)                                                                        gTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTc                                           <  1:2458218/62‑1 (MQ=255)                                                                        gTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCACGGAAATATGGCGTtg               >  1:2495915/1‑90 (MQ=255)                                                                        gTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCACGGAAATATGGCGTtg               >  1:679054/1‑90 (MQ=255)                                                                        gTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCACGGAAATATGGCGTtg               >  2:368299/1‑90 (MQ=255)                                                                        gTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCACGGAAATATGGCGTtg               >  2:1409297/1‑90 (MQ=255)                                                                          cACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATgg                                             >  1:2631170/1‑58 (MQ=255)                                                                          cACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATgg                                             <  2:2631170/58‑1 (MQ=255)                                                                          cACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCACGGAAATATGGCGTtgat             >  1:194105/1‑90 (MQ=255)                                                                          cACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCACGGAAATATGGCGTtgat             >  1:2755089/1‑90 (MQ=255)                                                                          cACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCACGGAAATATGGCGTtgat             >  1:317684/1‑90 (MQ=255)                                                                                tAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCACGGAAATATGGCGTTGATGAGTCg       >  2:1722847/1‑90 (MQ=255)                                                                                  aCATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCACGGAAATATGGCGTTGATGAGTCGCt     >  2:1700865/1‑90 (MQ=255)                                                                                     tGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCACGGAAATATGGCGTTGATGAGTCGCTGAt  >  1:1548506/1‑90 (MQ=255)                                                                                     tGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCACGGAAATATGGCGTTGATGAGTCGCTGAt  >  2:1234595/1‑90 (MQ=255)                                                                                          |                                                                                      GCAACTTCGCGGATTATCTGCTGAAAAACCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTGCCGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCACGGAAATATGGCGTTGATGAGTCGCTGAT  >  NZ_CP009273/3098246‑3098420

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: ‑