Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	3,876,435	T→A	I219F (ATC→TTC)	dnaA ←	chromosomal replication initiator protein DnaA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,876,435	0	T	A	100.0%	162.6 / NA	42	I219F (ATC→TTC)	dnaA	chromosomal replication initiator protein DnaA
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base A (21/21);  total (21/21)

GTTGATTACCTTCCAGCAGGGCGTTGAAGGTGTGGAAAAACTCTTCCTGAGATCGTTCTTTATTAGCAAAAAACTGAATATCGTCGATCAGCAGTGCATCTACGGAACGGTAGTAGCGTTTAAACTCTTCGATCGCGTTGTTTTGCAGGGCTTTAACCATGTCCTGAACAAAGCGCTCGGAGTGCATATAAACCACTTTGGCATTCGGCTTGCGCGCCATAATGCCGTTACCCACCGCATGCAGCAGGTGAGTTTTACC  >  NZ_CP009273/3876303‑3876561                                                                                                                                     |                                                                                                                               gTTGATTACCTTCCAGCAGGGCGTTGAAGGTGTGGAAAAACTCTTCCTGAGATCGTTCTTTATTAGCAAAAAACTGAATATCGTCGATCAGCAGTGCATCTACGGAACGGTAGTAGCGTTTAAACTCTTCGAACGCgtt                                                                                                                          >  1:617490/1‑139 (MQ=255)  ttGATTACCTTCCAGCAGGGCGTTGAAGGTGTGGAAAAACTCTTCCTGAGATCGTTCTTTATTAGCAAAAAACTGAATATCGTCGATCAGCAGTGCATCTACGGAACGGTAGTAGCGTTTAAACTCTTCGAAcgcg                                                                                                                            <  2:617490/136‑1 (MQ=255)         ccTTCCAGCAGGGCGTTGAAGGTGTGGAAAAACTCTTCCTGAGATCGTTCTTTATTAGCAAAAAACTGAATATCGTCGATCAGCAGTGCATCTACGGAACGGTAGTAGCGTTTAAACTCTTCGAACGCGTTGTTTTGCa                                                                                                                  <  1:559814/139‑1 (MQ=255)         ccTTCCAGCAGGGCGTTGAAGGTGTGGAAAAACTCTTCCTGAGATCGTTCTTTATTAGCAAAAAACTGAATATCGTCGATCAGCAGTGCATCTACGGAACGGTAGTAGCGTTTAAACTCTTCGAACGCGTTGTTTTGCa                                                                                                                  <  1:377936/139‑1 (MQ=255)            tCCAGCAGGGCGTTGAAGGTGTGGAAAAACTCTTCCTGAGATCGTTCTTTATTAGCAAAAAACTGAATATCGTCGATCAGCAGTGCATCTACGGAACGGTAGTAGCGTTTAAACTCTTCGAACGCGTTGTTTTGCAggg                                                                                                               >  1:571561/1‑139 (MQ=255)                    ggCGTTGAAGGTGTGGAAAAACTCTTCCTGAGATCGTTCTTTATTAGCAAAAAACTGAATATCGTCGATCAGCAGTGCATCTACGGAACGGTAGTAGCGTTTAAACTCTTCGAACGCGTTGTTTTGCAGGGCTTTAAc                                                                                                        >  2:31352/1‑138 (MQ=255)                      cGTTGAAGGTGTGGAAAAACTCTTCCTGAGATCGTTCTTTATTAGCAAAAAACTGAATATCGTCGATCAGCAGTGCATCTACGGAACGGTAGTAGCGTTTAAACTCTTCGAACGCGTTGTTTTGCAGGGCTTTAACCAt                                                                                                     >  2:278390/1‑139 (MQ=255)                                gtgGAAAAACTCTTCCTGAGATCGTTCTTTATTAGCAAAAAACTGAATATCGTCGATCAGCAGTGCATCTACGGAACGGTAGTAGCGTTTAAACTCTTCGAACGCGTTGTTTTGCAGGGCTTTAACCATGTc                                                                                                  >  2:63167/1‑132 (MQ=255)                                gtgGAAAAACTCTTCCTGAGATCGTTCTTTATTAGCAAAAAACTGAATATCGTCGATCAGCAGGGCATCTACGGAACGGTAGTAGCGTTTAAACTCTTCGAACGCGTTGTTTTGCAGGGCTTTAACCATGTc                                                                                                  <  1:63167/132‑1 (MQ=255)                                   gAAAAACTCTTCCTGAGATCGTTCTTTATTAGCAAAAAACTGAATATCGTCGATCAGCAGTGCATCTACGGAACGGTAGTAGCGTTTAAACTCTTCGAACGCGTTGTTTTGCAGGGCTTTAACCATGTCCTGAACAAAg                                                                                        <  1:179951/139‑1 (MQ=255)                                        aCTCTTCCTGAGATCGTTCTTTATTAGCAAAAAACTGAATATCGTCGATCAGCAGTGCATCTACGGAACGGTAGTAGCGTTTAAACTCTTCGAACGCGTTGTTTTGCAGGGCTTTAACCATGTCCTGAACAAAGCGCTc                                                                                   <  1:278390/139‑1 (MQ=255)                                                    aTCGTTCTTTATTAGCAAAAAACTGAATATCGTCGATCAGCAGTGCATCTACGGAACGGTAGTAGCGTTTAAACTCTTCGAACGCGTTGTTTTGCAGGGCTTTAACCATGTCCTGAACAAAGCGCTCGGAGt                                                                              <  1:330273/132‑1 (MQ=255)                                                    aTCGTTCTTTATTAGCAAAAAACTGAATATCGTCGATCAGCAGTGCATCTACGGAACGGTAGTAGCGTTTAAACTCTTCGAACGCGTTGTTTTGCAGGGCTTTAACCATGTCCTGAACAAAGCGCTCGGAGt                                                                              >  2:330273/1‑132 (MQ=255)                                                        ttCTTTATTAGCAAAAAACTGAATATCGTCGATCAGCAGTGCATCTACGGAACGGTAGTAGCGTTTAAACTCTTCGAACGCGTTGTTTTGCAGGGCTTTAACCATGTCCTGAACAAAGCGCTCGGAGTGCATATAAAc                                                                    >  1:96196/1‑138 (MQ=255)                                                                  gCAAAAAACTGAATATCGTCGATCAGCAGTGCATCTACGGAACGGTAGTAGCGTTTAAACTCTTCGAACGCGTTGTTTTGCAGGGCTTTAACCATGTCCTGAACAAAGCGCTCGGAGTGCATATAAACCACTTTGGCAt                                                         >  2:437649/1‑139 (MQ=255)                                                                   cAAAAAACTGAATATCGTCGATCAGCAGTGCATCTACGGAACGGTAGTAGCGTTTAGACTCTTCGAACGCGTTGTTTTGCAGGGCTTTAACCATGTCCTGAACAAAGCGCTCGGAGTGCATATAAACCACTTTGGCAtt                                                        >  1:639161/1‑139 (MQ=255)                                                                   cAAAAAACTGAATATCGTCGATCAGCAGTGCATCTACGGAACGGTAGTAGCGTTTAAACTCTTCGAACGCGTTGTTTTGCAGGGCTTTAACCATGTCCTGAACAAAGCGCTCGGAGTGCATATAAACCACtt                                                               <  1:200075/132‑1 (MQ=255)                                                                   cAAAAAACTGAATATCGTCGATCAGCAGTGCATCTACGGAACGGTAGAAGCGTTTAAACTCTTCGAACGCGTTGTTTTGCAGGGCTTTAACCATGTCCTGAACAAAGCGCTCGGAGTGCATATAAACCACtt                                                               >  2:200075/1‑132 (MQ=255)                                                                             aaTATCGTCGATCAGCAGTGCATCTACGGAACGGTAGTAGCGTTTAAACTCTTCGAACGCGTTGTTTTGCAGGGCTTTAACCATGTCCTGAACAAAGCGCTCGGAGTGCATATAAACCACTTTGGCATTCGGCTTgcg                                               <  2:571561/138‑1 (MQ=255)                                                                                    tcgATCAGCAGTGCATCTACGGAACGGTAGTAGCGTTTAAACTCTTCGAACGCGTTGTTTTGCAGGGCTTTAACCATGTCCTGAACAAAGCGCTCGGAGTGCATATAAACCACTTTGGCATTCGGCTTGCGCGCCATaa                                       <  2:154118/139‑1 (MQ=255)                                                                                       aTCAGCAGTGCATCTACGGAACGGTAGTAGCGTTTAAACTCTTCGAACGCGTTGTTTTGCAGGGCTTTAAcc                                                                                                       >  1:311879/1‑72 (MQ=255)                                                                                       aTCAGCAGTGCATCTACGGAACGGTAGTAGCGTTTAAACTCTTCGAACGCGTTGTTTTGCAGGGCTTTAAcc                                                                                                       <  2:311879/72‑1 (MQ=255)                                                                                       aTCAGCAGTGCATCTACGGAACGGTAGTAGCGTTTAAACTCTTCGAACGCGTTGTTTTGCAGGGCTTTAACCATGTCCTGAACAAAGCGCTCGGAGTGCATATAAACCACTTTGGCATTCGGCTTGCGCGCCATAATGc                                    >  1:29070/1‑139 (MQ=255)                                                                                            cagTGCATCTACGGAACGGTAGTAGCGTTTAAACTCTTCGAACGCGTTGTTTTGCAGGGCTTTAACCATGTCCTGAACAAAGCGCTCGGAGTGCATATAAACCACTTTGGCATTCGGCTTgcg                                               <  2:311047/123‑1 (MQ=255)                                                                                            cagTGCATCTACGGAACGGTAGTAGCGTTTAAACTCTTCGAACGCGTTGTTTTGCAGGGCTTTAACCATGTCCTGAACAAAGCGCTCGGAGTGCATATAAACCACTTTGGCATTCGGCTTgcg                                               >  1:311047/1‑123 (MQ=255)                                                                                               tGCATCTACGGAACGGTAGTAGCGTTTAAACTCTTCGAACGCGTTGTTTTGCAGGGCTTTAACCATGTCCTGAACAAAGCGCTCGGAGTGCATATAAACCACTTTGGCATTCGGCTTGCGCGCCATAATGCCGTTAccc                            <  2:22650/139‑1 (MQ=255)                                                                                                      aCGGAACGGTAGTAGCGTTTAAACTCTTCGAACGCGTTGTTTTGCAGGGCTTTAACCATGTCCTGAACAAAGCGCTCGGAGTGCATATAAACCACTTTGGCATTCGGCTTGCGCGCCATAATGCCGTTACCCACCGCAt                     >  2:48162/1‑139 (MQ=255)                                                                                                       cGGAACGGTAGTAGCGTTTAAACTCTTCGAACGCGTTGTTTTGCAGGGCTTTAACCATGTCCTGAACAAAGCGCTCGGAGTGCATATAAACCACTTTGGCATTCGGCTTGCGCGCCATAATGCCGTTACCCACCGCa                      <  2:523254/137‑1 (MQ=255)                                                                                                         gAACGGTAGTAGCGTTTAAACTCTTCGAACGCGTTGTTTTGCAGGGCTTTAACCATGTCCTGAACAAAGCGCTCGGAGTGCATATAAACCACTTTGGCATTCGGCTTgcg                                               <  2:281028/110‑1 (MQ=255)                                                                                                         gAACGGTAGTAGCGTTTAAACTCTTCGAACGCGTTGTTTTGCAGGGCTTTAACCATGTCCTGAACAAAGCGCTCGGAGTGCATATAAACCACTTTGGCATTCGGCTTgcg                                               >  1:327750/1‑110 (MQ=255)                                                                                                         gAACGGTAGTAGCGTTTAAACTCTTCGAACGCGTTGTTTTGCAGGGCTTTAACCATGTCCTGAACAAAGCGCTCGGAGTGCATATAAACCACTTTGGCATTCGGCTTgcg                                               <  2:327750/110‑1 (MQ=255)                                                                                                         gAACGGTAGTAGCGTTTAAACTCTTCGAACGCGTTGTTTTGCAGGGCTTTAACCATGTCCTGAACAAAGCGCTCGGAGTGCATATAAACCACTTTGGCATTCGGCTTgcg                                               >  1:281028/1‑110 (MQ=255)                                                                                                               tagtagCGTTTAAACTCTTCGAACGCGTTGTTTTGCAGGGCTTTAACCATGTCCTGAACAAAGCGCTCGGAGTGCATATAAACCACTTTGGCATTCGGCTTGCGCGCCATAATGCCGTTACCCACCGCATGCAGCAGGt            <  2:414462/139‑1 (MQ=255)                                                                                                                    gCGTTTAAACTCTTCGAACGCGTTGTTTTGCAGGGCTTTAACCATGTCCTGAACAAAGCGCTCGGAGTGCATATAAACCACTTTGGCATTCGGCTTGCGCGCCATAATGCCGTTACCCACCGCATGCAGCAGGTGAGtt       >  1:168404/1‑139 (MQ=255)                                                                                                                       tttAAACTCTTCGAACGCGTTGTTTTGCAGGGCTTTAACCATGTCCTGAACAAAGCGCTc                                                                                   >  2:353412/1‑60 (MQ=255)                                                                                                                       tttAAACTCTTCGAACGCGTTGTTTTGCAGGGCTTTAACCATGTCCTGAACAAAGCGCTc                                                                                   <  1:353412/60‑1 (MQ=255)                                                                                                                       tttAAACTCTTCGAACGCGTTGTTTTGCAGGGCTTTAACCATGTCCTGAACAAAGCGCTCGGAGTGCATATAAACCACTTTGGCATTCGGCTTGCGCGCCATAATGCCGtt                                <  2:444955/111‑1 (MQ=255)                                                                                                                       tttAAACTCTTCGAACGCGTTGTTTTGCAGGGCTTTAACCATGTCCTGAACAAAGCGCTCGGAGTGCATATAAACCACTTTGGCATTCGGCTTGCGCGCCATAATGCCGtt                                >  1:444955/1‑111 (MQ=255)                                                                                                                       tttAAACTCTTCGAACGCGTTGTTTTGCAGGGCTTTAACCATGTCCTGAACAAAGCGCTCGGAGTGCATATAAACCACTTTGGCATTCGGCTTGCGCGCCATAATGCCGTTACCCACCGCATGCAGCAGGTGAGTTTTa    >  2:496278/1‑139 (MQ=255)                                                                                                                          aaaCTCTTCGAACGCGTTGTTTTGCAGGGCTTTAACCATGTCCTGAACAAAGCGCTCGGAGTGCATATAAACCACTTTGGCATTCGGCTTGCGCGCCATAATGCCGTTACCCACCGCATGCAGCAGGTGAGTTTTAcc  <  1:437649/138‑1 (MQ=255)                                                                                                                                ttCGAACGCGTTGTTTTGCAGGGCTTTAACCATGTCCTGAACAAAGCGCTCGGAGTGCATATAAACCACTTTGGCATTCGGCTTgcg                                               >  1:576198/1‑87 (MQ=255)                                                                                                                                ttCGAACGCGTTGTTTTGCAGGGCTTTAACCATGTCCTGAACAAAGCGCTCGGAGTGCATATAAACCACTTTGGCATTCGGCTTgcg                                               <  2:576198/87‑1 (MQ=255)                                                                                                                                     |                                                                                                                               GTTGATTACCTTCCAGCAGGGCGTTGAAGGTGTGGAAAAACTCTTCCTGAGATCGTTCTTTATTAGCAAAAAACTGAATATCGTCGATCAGCAGTGCATCTACGGAACGGTAGTAGCGTTTAAACTCTTCGATCGCGTTGTTTTGCAGGGCTTTAACCATGTCCTGAACAAAGCGCTCGGAGTGCATATAAACCACTTTGGCATTCGGCTTGCGCGCCATAATGCCGTTACCCACCGCATGCAGCAGGTGAGTTTTACC  >  NZ_CP009273/3876303‑3876561

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑