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%	176.6 / NA	41	coding (544/1080 nt)	mltC	membrane‑bound lytic murein transglycosylase MltC
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base . (21/20);  total (21/20)

CTTCGCGGATTATCTGCTGAAAAACCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTGCCGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCACGGAAATATGGCGTTGATGAGT  >  NZ_CP009273/3098250‑3098413                                                                                      |                                                                               cTTCGCGGATTATCTGCTGAAAAACCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTGcgaac                                                                            >  2:717911/1‑86 (MQ=255)  ttCGCGGATTATCTGCTGAAAAACCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAacc                                                                          >  1:51230/1‑90 (MQ=255)  ttCGCGGATTATCTGCTGAAAAACCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAacc                                                                          >  1:320189/1‑90 (MQ=255)     gcgGATTATCTGCTGAAAAACCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAaccacc                                                                       <  1:44258/90‑1 (MQ=255)     gcgGATTATCTGCTGAAAAACCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAaccacc                                                                       <  1:212668/90‑1 (MQ=255)     gcgGATTATCTGCTGAAAAACCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAaccacc                                                                       <  2:2008/90‑1 (MQ=255)                  tgAAAAACCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTgc                                                          <  2:201763/90‑1 (MQ=255)                    aaaaaCCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTgcgc                                                        <  1:717911/90‑1 (MQ=255)                    aaaaaCCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTgcgc                                                        <  1:289468/90‑1 (MQ=255)                         ccGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACaaa                                                   <  1:131037/90‑1 (MQ=255)                         ccGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACaaa                                                   <  2:747835/90‑1 (MQ=255)                          cGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTGcgaa                                                                             >  1:516552/1‑61 (MQ=255)                          cGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTGcgaa                                                                             <  2:516552/64‑4 (MQ=255)                          cGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAat                                                  >  2:1124028/1‑90 (MQ=255)                           gTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAaccacc                                                                       <  1:783522/68‑1 (MQ=255)                           gTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAaccacc                                                                       >  2:783522/1‑68 (MQ=255)                             cTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATAtc                                               >  1:915508/1‑90 (MQ=255)                                   agCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCa                                         <  1:291293/90‑1 (MQ=255)                                    gCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCAt                                        >  2:740599/1‑90 (MQ=255)                                         agcaACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTcc                                   >  1:489923/1‑90 (MQ=255)                                                ggCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGc                            <  2:489923/90‑1 (MQ=255)                                                  cTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGt                          >  2:987328/1‑90 (MQ=255)                                                    gCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCa                        >  2:634405/1‑90 (MQ=255)                                                     cGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCAc                       <  1:1099829/90‑1 (MQ=255)                                                     cGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCAc                       <  1:259610/90‑1 (MQ=255)                                                       tATCATCTACAGCGTCCCCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCACgg                     <  2:169533/90‑1 (MQ=255)                                                         tcatcTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCACGGaa                   >  2:225985/1‑90 (MQ=255)                                                         tcatcTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCACGGaa                   >  2:433647/1‑90 (MQ=255)                                                          catcTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATAtc                                               <  1:419960/61‑1 (MQ=255)                                                          catcTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATAtc                                               >  2:419960/1‑61 (MQ=255)                                                             cTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCACGGAAatat               <  1:1019773/90‑1 (MQ=255)                                                              tACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCACGGAAATATg              >  2:913699/1‑90 (MQ=255)                                                              tACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCACGGAAATATg              >  1:552972/1‑90 (MQ=255)                                                              tACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCACGGAAATATg              >  1:744783/1‑90 (MQ=255)                                                                cAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCACGGAAATATGGc            >  2:334074/1‑90 (MQ=255)                                                                     tCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATg                                       >  2:808885/1‑58 (MQ=255)                                                                     tCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATg                                       <  1:808885/58‑1 (MQ=255)                                                                     tCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTc                                    <  1:688710/61‑1 (MQ=255)                                                                     tCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTc                                    >  2:688710/1‑61 (MQ=255)                                                                      cACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCACGGAAATATGGCGTtgat      >  1:831063/1‑90 (MQ=255)                                                                       aCCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCACGGAAATATGGCGTtgatg     >  1:941775/1‑90 (MQ=255)                                                                       aCCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCACGGAAATATGGCGTtgatg     <  2:697487/90‑1 (MQ=255)                                                                       aCCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCACGGAAATATGGCGTtgatg     <  2:51230/90‑1 (MQ=255)                                                                          aTTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCACGGAAATATGGCGTTGATGAGt  >  1:1042812/1‑90 (MQ=255)                                                                                      |                                                                               CTTCGCGGATTATCTGCTGAAAAACCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTGCCGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCACGGAAATATGGCGTTGATGAGT  >  NZ_CP009273/3098250‑3098413

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑