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%	88.6 / NA	27	E67G (GAA→GGA)	hflD	high frequency lysogenization protein HflD
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (7/20);  total (7/20)

CCCAGAGTGTCGAGCGCGCCTTTCGCTGAGGAGAGTTTGCGCTCAAGCACCATCAAGCTGAGTGTGTAGCGGGTTAATTCGGCGTTTAAGCCCTGGCGACTGCTGGCATTGAGCACGCCGAGCAGGGTTTCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGCCAGCGTCGAGCTGGGGTTCATATCAATAATACTGTTGAGTGAGACGTGTAGCGCATCGGCATCACAATGCCCCTGGTGAGCGAGTTGTTGCA  >  NZ_CP009273/1187759‑1188023                                                                                                                                  |                                                                                                                                        cccAGAGTGTCGAGCGCGCCTTTCGCTGAGGAGAGTTTGCGCTCAAGCACCATCAAGCTGAGTGTGTAGCGGGTTAATTCGGCGTTTAAGCCCTGGCGACTGCTGGCATTGAGCACGCCGAGCAGGGTTCCCAGCCCg                                                                                                                                 <  2:557072/138‑1 (MQ=255)          tCGAGCGCGCCTTTCGCTGAGGAGAGTTTGCGCTCAAGCACCATCAAGCTGAGTGTGTAGCGGGTTAATTCGGCGTTTAAGCCCTGGCGACTGCTGGCATTGAGCACGCCGAGCAGGGTTCCCAGCCCGACGCGCAgg                                                                                                                        <  2:596917/138‑1 (MQ=255)                gcgcCTTTCGCTGAGGAGAGTTTGCGCTCAAGCACCATCAAGCTGAGTGTGTAGCGGGTTAATTCGGCGTTTAAGCCCTGGCGACTGCTGGCATTGAGCACGCCGAGCAGGGTTCCCAGCCCGACGCGCAGGTTGGCtt                                                                                                                 >  1:118483/1‑139 (MQ=255)                       tCGCTGAGGAGAGTTGGCGCTCAAGCACCATCAAGCTGAGTGTGTAGCGGGTTAATTCGGCGTTTAAGCCCTGGCGACTGCTGGCATTGAGCACGCCGAGCAGGGTTCCCAGCCCGACGCGCAGGTTGGCTTCGCTa                                                                                                            <  2:437514/137‑1 (MQ=255)                              ggagATTTTGCGCTAAAGCCCCATCAAGCTGAGTGTGTAGCGGGTTAATTCGGCGTTTAAGCCCTGGCGACTGCTGGCATTGAGCACGCCGAGCAGGGTTCCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCAaaaa                                                                                                   <  2:667904/139‑1 (MQ=255)                                   gTTTGCGCTCAAGCACCATCAAGCTGAGTGTGTAGCGGGTTAATTCGGCGTTTAAGCCCTGGCGACTGCTGGCATTGAGCACGCCGAGCAGGGTTCCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGc                                                                                              <  1:539210/139‑1 (MQ=255)                                       gcgcTCAAGCACCATCAAGCTGAGTGTGTAGCGGGTTAATTCGGCGTTTAAGCCCTGGCGACTGCTGGCATTGAGCACGCCGAGCAGGGTTCCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGCCAGc                                                                                          >  1:351597/1‑139 (MQ=255)                                        cgcTCAAGCACCATCAAGCTGAGTGTGTAGCGGGTTAATTCGGCGTTTAAGCCCTGGCGACTGCTGGCATTGAGCACGCCGAGCAGGGTTCCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGCCAGCg                                                                                         <  1:812711/139‑1 (MQ=255)                                          cTCAAGCACCATCAAGCTGAGTGTGTAGCGGGTTAATTCGGCGTTTAAGCCCTGGCGACTGCTGGCATTGAGCCCGCCGAGCAGGGTTCCCAGCCCGCCGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGCCAGCGTc                                                                                       <  2:117370/139‑1 (MQ=255)                                                       aaGCTGAGTGTGTAGCGGTTTAATTCGGCGTTTAAGCCCTGGCGACTGCGGGCATTGAGCCCGCCGAGCAGGGTTCCCAGCCCGACGCGCGGGTTGGCTTCGCTACCGCCAAAAACCGCCAGCGTCGAGCTGGGGTTc                                                                           <  2:427649/138‑1 (MQ=255)                                                        agttGAGTGTATAGCGGGTTAATGCGGCGTTAAAGCCCTGGCGCCTGATGCCATTGAGCACGCCGAACAGGGTCCCCAGCCCGACGCGCAGGTTGGCTTCGCTCCCGCCAAAAACCGCCAGCGTCGAGCTGGGGTTCat                                                                         <  2:118483/136‑1 (MQ=255)                                                        aGCTGAGTGTGTAGCGGTTTAATTCGGCGTTTAAGCCCTGGCGACTGCTGGCATTGAGCACGCCGAGCAGGGTTCCCAGCCCGACGCGCAGGTTGGTTTCGCTACCGCCAAAAACCGCCAGCGTCGAGCTGGGGTTCat                                                                         <  2:96809/139‑1 (MQ=255)                                                          cTGAGTGTGTAGCGGGTTAATTCGGCGTTTAAGCCCTGGCGCCTGCTGGCATTGAGCACGCCGAGCAGGGTTCCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGCCAGCGTCGAGCTGGGGTTCatat                                                                       <  1:694753/139‑1 (MQ=255)                                                                 tgtAGCGGGTTAATTCGGCGTTTAAGCCCTGGCGACTGCTGGCATTGAGCACGCCGAGCAGGGTTCCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGCCAGCGTCGAGCTGGGGTTCATATCaataat                                                                <  2:299886/139‑1 (MQ=255)                                                                            aaTTCGGCGTTTAAGCCCTGGCGACTGCTGGCATTGAGCACGCCGAGCGGGGTTCCCAGCCCGCCGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGCCAGCGTCGAGCTGGGGTTCATATCAATAATACTGTtgagt                                                      <  1:240311/138‑1 (MQ=255)                                                                             aTTCGGCGTTTAAGCCCTGGCGACTGCTGGCATTGAGCACGCCGAGCAGGGTTCCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGCCAGCGTCGAGCTGGGGTTCATATCAATAATACTGTtgagt                                                      >  1:385583/1‑137 (MQ=255)                                                                             aTTCGGCGTTTAAGCCCTGGCGACTGCTGGCATTGAGCACGCCGAGCAGGGTTCCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGCCAGCGTCGAGCTGGGGTTCATATCAATAATACTGTtgagt                                                      >  1:319480/1‑137 (MQ=255)                                                                                    gTTTAAGCCCTGGCGACTGCTGGCATTGAGCACGCCGAGCAGGGTTCCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGCCAGCGTCGAGCTGGGGTTCATATCAATAATACTGTTGAGTGAGACgtgt                                             <  2:319480/139‑1 (MQ=255)                                                                                    gTTTAAGCCCTGGCGACTGCTGGCATTGAGCACGCCGAGCAGGGTTCCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGCCAGCGTCGAGCTGGGGTTCATATCAATAATACTGTTGAGTGAGACgtgt                                             <  2:385583/139‑1 (MQ=255)                                                                                           cccTGGCGACTGCTGGCATTGAGCACGCCGAGCAGGGTTCCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCAAAAAACCGCCAGCGTCGAGCTGGGGTTCATATCAATAATACTGTTGAGTGAGACGTGTAGCGCAt                                      <  2:106518/139‑1 (MQ=255)                                                                                               ggCGACTGCTGGCATTGAGCACGCCGAGCAGGGTTCCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGCCAGCGTCGAGCTGGGGTTCATATCAATAATACTGTTGAGTGAGACGTGTAGCGCATCgg                                   >  1:543544/1‑138 (MQ=255)                                                                                                gCGACTGCTGGCATTGAGCACGCCGAGCAGGGTTCCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGCCAGCGTCGAGCTGGGGTTCATATCAATAATACTGTTGAGTGAGACGTGTAGCGCATCGGCa                                 <  2:351597/139‑1 (MQ=255)                                                                                                       ctgGCATTGAGCACGCCGAGCAGGGTTCCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGCCAGCGTCGAGCTGGGGTTCATATCAATAATACTGTTGAGTGAGACGTGTAGCGCATCGGCATCACaa                           <  2:543544/138‑1 (MQ=255)                                                                                                            aTTGAGCACGCCGAGCAGGGTCCCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGCCAGCGTCGAGCTGGGGTTCATATCAATAATACTGTTGAGTGAGACGTGTAGCGCATCGGCATCACAATGcccc                     <  2:442068/139‑1 (MQ=255)                                                                                                                    cGCCGAGCAGGGTTCCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGCCAGCGTCGAGCTGGGGTTCat                                                                         >  1:741269/1‑79 (MQ=255)                                                                                                                    cGCCGAGCAGGGTTCCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGCCAGCGTCGAGCTGGGGTTCat                                                                         <  2:741269/79‑1 (MQ=255)                                                                                                                               gTTCCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGCCAGCGTCGAGCTGGGGTTCATATCAATAATACTGTTGAGTGAGACGTGTAGCGCATCGGCATCACAATGCCCCTGGTGAGCGAGTTGTTGCa  >  1:206100/1‑139 (MQ=255)                                                                                                                                  |                                                                                                                                        CCCAGAGTGTCGAGCGCGCCTTTCGCTGAGGAGAGTTTGCGCTCAAGCACCATCAAGCTGAGTGTGTAGCGGGTTAATTCGGCGTTTAAGCCCTGGCGACTGCTGGCATTGAGCACGCCGAGCAGGGTTTCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGCCAGCGTCGAGCTGGGGTTCATATCAATAATACTGTTGAGTGAGACGTGTAGCGCATCGGCATCACAATGCCCCTGGTGAGCGAGTTGTTGCA  >  NZ_CP009273/1187759‑1188023

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑