Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	1,187,888	T→C	E67G (GAA→GGA)	hflD ←	high frequency lysogenization protein HflD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,187,888	0	T	C	100.0%	109.3 / NA	31	E67G (GAA→GGA)	hflD	high frequency lysogenization protein HflD
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (12/19);  total (12/19)

CAAGCACCATCAAGCTGAGTGTGTAGCGGGTTAATTCGGCGTTTAAGCCCTGGCGACTGCTGGCATTGAGCACGCCGAGCAGGGTTTCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGCCAGCGTCGAGCTGGGGTTCATATCAATAATACTGTTGAGTGAGA  >  NZ_CP009273/1187802‑1187975                                                                                       |                                                                                        cAAGCACCATCAAGCTGAGTGTGTAGCGGGTTAATTCGGCGTTTAAGCCCTGGCGACTGCTGGCATTGAGCACGCCGAGCAGGGTTCCCAg                                                                                     >  1:556099/1‑91 (MQ=255)      aCCATCAAGCTGAGTGTGTAGCGGGTTAATTCGGCGTTTAAGCCCTGGCGACTGCTGGCATTGAGCACGCCGAGCAGGGTTCCCAGCCCGa                                                                                >  2:72242/1‑91 (MQ=255)         aTCAAGCTGAGTGTGTAGCGGGTTAATTCGGCGTTTAAGCCCTGGCGACTGCTGGCATTGAGCACGCCGAGCAGGGTTCCCAGCCCGAcgc                                                                             >  1:846745/1‑91 (MQ=255)           cAAGCTGAGTGTGTAGCGGGTTAATTCGGCGTTTAAGCCCTGGCGACTGCTGGCATTGAGCACGCCGAGCAGGGTTCCCAGCCCGACgcgc                                                                           <  1:634351/91‑1 (MQ=255)             aGCTGAGAGTGTAGCGGGTTAATTCGGCGTTTAAGCCCTGGCGACCGCTGGCATTGAGCACGCCGAGCAGGGTTCCCAGCCCGACGCGCAg                                                                         >  2:471441/1‑91 (MQ=255)                 gAGTGTGTAGCGGGTTAATTCGGCGTTTAAGCCCTGGCGACTGCTGGCATTGAGCACGCCGAGCAGGGTTCCCAGCCCGACGCGCAGGTTg                                                                     >  1:13993/1‑91 (MQ=255)                        tAGCGGGTTAATTCGGCGTTTAAGCCCTGGCGACTGCTGGCATTGAGCACGCCGAGCAGGGTTCCCAGCCCGACGCGCAGGTTGGCTTCGc                                                              >  1:62577/1‑91 (MQ=255)                             ggTTAATTCGGCGTTTAAGCCCTGGCGACTGCTGGCATTGAGCACGCCGAGCAGGGTTCCCAGCCCGACGCGCAGGTTGGCTTCGCTACCg                                                         >  1:428772/1‑91 (MQ=255)                               ttAATTCGGCGTTTAAGCCCTGGCGACTGCTGGCATTGAGCACGCCGAGCAGGGTTCCCAGCCCGACgcgc                                                                           <  1:443177/71‑1 (MQ=255)                               ttAATTCGGCGTTTAAGCCCTGGCGACTGCTGGCATTGAGCACGCCGAGCAGGGTTCCCAGCCCGACgcgc                                                                           >  2:443177/1‑71 (MQ=255)                                    tCGGCGTTTAAGCCCTGGCGACTGCTGGCATTGAGCACGCCGAGCAGGGTTCCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCaaaaa                                                  <  2:737794/91‑1 (MQ=255)                                                   tGGCGACTGCTGGCATTGCGCACGCCGAGCAGGGTTCCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGCCAGCGTCGAGc                                   >  1:680765/1‑91 (MQ=255)                                                   tGGCGACTGCTGGCATTGAGCACGCCGAGCAGGGTTCCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGCCAGCGTCGAGc                                   >  2:518749/1‑91 (MQ=255)                                                     gCGACTGCTGGCATTGAGCACGCCGAGCAGGGTTCCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGCCAGCGTCGAGCTg                                 <  2:699744/91‑1 (MQ=255)                                                      cGACTGCTGGCATTGAGCACGCCGAGCAGGGTTCCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGCCAGCGTCGAGCTgg                                <  2:680765/91‑1 (MQ=255)                                                      cGACTGCTGGCATTGAGCACGCCGAGCAGGGTTCCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGCCAGCGTCGAGCTgg                                <  1:74687/91‑1 (MQ=255)                                                         ctgctgGCATTGAGCACGCCGAGCAGGGTTCCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGCCAGCGTCGAGCTGGGGt                             <  1:770455/91‑1 (MQ=255)                                                             tgGCATTGAGCACGCCGAGCAGGGTTCCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCC‑AAAACCGCCAGCGTCGAGCTGGGGTTCata                        <  2:604043/91‑1 (MQ=255)                                                              ggCATTGAGCACGCCGAGCAGGGTTCCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGCCAGCGTCGAGCTGGGGTTCata                        <  1:733331/91‑1 (MQ=255)                                                              ggCATTGAGCACGCCGAGCAGGGTTCCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGCCAGCGTCGAGCTGGGGTTCata                        <  2:556099/91‑1 (MQ=255)                                                              ggCATTGAGCACGCCGAGCAGGGTTCCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGCCAGCGTCGAGCTGGGGTTCata                        <  2:62577/91‑1 (MQ=255)                                                              ggCATTGAGCACGCCGAGCAGGGTTCCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGCCAGCGTCGAGCTGGGGTTCata                        <  1:72242/91‑1 (MQ=255)                                                                 aTTGAGCACGCCGAGCAGGGTTCCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGCCAGCGTCGAGCTGGGGTTCATATCa                     <  1:744059/91‑1 (MQ=255)                                                                    gAGCACGCCGAGCAGGGTTCCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGCCAGCGTCGAGCTGGGGTTCATATCaata                  >  1:772132/1‑91 (MQ=255)                                                                        aCGCCGAGCAGGGTTCCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGCCAGCGTCGAGCTGGGGTTCATATCAATAATAc              <  2:309450/91‑1 (MQ=255)                                                                        aCGCCGAGCAGGGTTCCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGCCAGCGTCGAGCTGGGGTTCATATCAATAATAc              <  1:733858/91‑1 (MQ=255)                                                                            cGAGCAGGGTTCCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGCCAGCGTCGAGCTGGGGTTCATATCAATAATACTGtt          <  2:844829/91‑1 (MQ=255)                                                                              aGCAGGGTTCCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGCCAGCGTCGAGCTGGGGTTCATATCAATAATACTGTtga        >  1:26579/1‑91 (MQ=255)                                                                                 aGGGTTCCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGCCAGCGTCGAGCTGGGGTTCATATCAATAATACTGTtgagtg     <  2:674988/91‑1 (MQ=255)                                                                                 aGGGTTCCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGCCAGCGTCGAGCTGGGGTTCATATCAATAATACTGTtgagtg     <  2:421301/91‑1 (MQ=255)                                                                                    gTTCCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGCCAGCGTCGAGCTGGGGTTCATATCAATAATACTGTTGAGTgaga  <  1:442301/91‑1 (MQ=255)                                                                                       |                                                                                        CAAGCACCATCAAGCTGAGTGTGTAGCGGGTTAATTCGGCGTTTAAGCCCTGGCGACTGCTGGCATTGAGCACGCCGAGCAGGGTTTCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGCCAGCGTCGAGCTGGGGTTCATATCAATAATACTGTTGAGTGAGA  >  NZ_CP009273/1187802‑1187975

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑