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%	123.0 / NA	30	coding (544/1080 nt)	mltC	membrane‑bound lytic murein transglycosylase MltC
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base . (14/16);  total (14/16)

AACTTCGCGGATTATCTGCTGAAAAACCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTGCCGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCACGGAAATATGGCGTTGATGAGTCGCTGAT  >  NZ_CP009273/3098248‑3098420                                                                                        |                                                                                      aaCTTCGCGGATTATCTGCTGAAAAACCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTGcga                                                                                     <  2:875540/90‑3 (MQ=255)    ttCGCGGATTATCTGCTGAAAAACCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAacc                                                                                 <  1:37370/90‑1 (MQ=255)     tCGCGGATTATCTGCTGAAAAACCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAacca                                                                                <  1:285493/90‑1 (MQ=255)     tCGCGGATTATCTGCTGAAAAACCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAacca                                                                                <  1:287119/90‑1 (MQ=255)       gcgGATTATCTGCTGAAAAACCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAaccacc                                                                              <  2:596655/90‑1 (MQ=255)       gcgGATTATCTGCTGAAAAACCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAaccacc                                                                              <  2:822577/90‑1 (MQ=255)       gcgGATTATCTGCTGAAAAACCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAaccacc                                                                              <  2:336643/90‑1 (MQ=255)       gcgGATTATCTGCTGAAAAACCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAaccacc                                                                              <  2:827757/90‑1 (MQ=255)       gcgGATTATCTGCTGAAAAACCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAaccacc                                                                              <  1:707697/90‑1 (MQ=255)            ttATCTGCTGAAAAACCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGAt                                                                         >  1:85901/1‑90 (MQ=255)            ttATCTGCTGAAAAACCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGAt                                                                         >  2:442842/1‑90 (MQ=255)                    tgAAAAACCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTgc                                                                 <  1:551470/90‑1 (MQ=255)                      aaaaaCCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTgcgc                                                               <  1:625929/90‑1 (MQ=255)                            cGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAat                                                         >  2:789026/1‑90 (MQ=255)                             gTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAata                                                        >  1:49230/1‑90 (MQ=255)                                 gAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATAtctc                                                    >  1:178002/1‑90 (MQ=255)                                    gagCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGc                                                 <  1:520160/90‑1 (MQ=255)                                           agcaACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTcc                                          >  1:783695/1‑90 (MQ=255)                                              aaCGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGcc                                       <  1:93567/90‑1 (MQ=255)                                                  ggCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGc                                   <  2:146358/90‑1 (MQ=255)                                                    cTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGt                                 >  1:469311/1‑90 (MQ=255)                                                       cGTACCATCTACAGCGTCACCATTAACATGGTG‑CGAACCCCCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCAc                              <  1:738839/90‑1 (MQ=255)                                                                  cAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCACGGAAATATGGc                   >  2:617888/1‑90 (MQ=255)                                                                    gCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCACGGAAATATGGCGt                 >  2:893639/1‑90 (MQ=255)                                                                    gCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCACGGAAATATGGCGt                 >  2:49857/1‑90 (MQ=255)                                                                    gCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCACGGAAATATGGCGt                 >  1:822021/1‑90 (MQ=255)                                                                    gCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCACGGAAATATGGCGt                 >  1:570698/1‑90 (MQ=255)                                                                     cGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCAc                              >  1:886231/1‑76 (MQ=255)                                                                     cGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCAc                              <  2:886231/76‑1 (MQ=255)                                                                         aCCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCACGGAAATATGGCGTtgatg            <  2:499287/90‑1 (MQ=255)                                                                                   tGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCACGGAAATATGGCGTTGATGAGTCGCTGAt  >  2:524872/1‑90 (MQ=255)                                                                                        |                                                                                      AACTTCGCGGATTATCTGCTGAAAAACCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTGCCGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCACGGAAATATGGCGTTGATGAGTCGCTGAT  >  NZ_CP009273/3098248‑3098420

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑