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%	46.6 / NA	14	E67G (GAA→GGA)	hflD	high frequency lysogenization protein HflD
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (6/8);  total (6/8)

GAGTGTCGAGCGCGCCTTTCGCTGAGGAGAGTTTGCGCTCAAGCACCATCAAGCTGAGTGTGTAGCGGGTTAATTCGGCGTTTAAGCCCTGGCGACTGCTGGCATTGAGCACGCCGAGCAGGGTTTCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGCCAGCGTCGAGCTGGGGTTCATATCAATAATACTGTTGAGTGAGACGTGTAGCGCATCGGCATCACAA  >  NZ_CP009273/1187763‑1187998                                                                                                                              |                                                                                                               gagTGTCGAGCGCGCCTTTCGCTGAGGAGAGTTTGCGCTCAAGCACCATCAAGCTGAGTGTGTAGCGGGTTAATTCGGCGTTTAAGCCCTGGCGACTGCTGGCATTGAGCACGCCGAGCAGGGTTCCCAGCCCGAcgcg                                                                                                   <  2:149009/139‑1 (MQ=255) gagTGTCGAGCGCGCCTTTCGCTGAGGAGAGTTTGCGCTCAAGCACCATCAAGCTGAGTGTGTAGCGGGTTAATTCGGCGTTTAAGCCCTGGCGACTGCTGGCATTGAGCACGCCGAGCAGGGTTCCCAGCCCGAcgcg                                                                                                   <  2:315779/139‑1 (MQ=255)                                    cgcTCAAGCACCATCAAGCTGAGTGTGTAGCGGGTTAATTCGGCGTTTAAGCCCTGGCGACTGCTGGCATTGAGCACGCCGAGCAGGGTTCCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGCCAGCg                                                                <  1:246127/139‑1 (MQ=255)                                          aGCACCATCAAGCTGAGTGTGTAGCGGGTTAATTCGGCGTTTAAGCCCTGGCGACTGCTGGCATTGAGCACGCCGAGCAGGGTTCCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGCCAGCGTCGAGc                                                          >  1:194637/1‑139 (MQ=255)                                                   aaGCTGAGGGTGTAGCGGGTTAATTCGGCGTTTAAGCCCTGGCGACTGCTGGCATGGAGCACGCCGAGCAGGGTTCCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGCCAGCGTCGAGCTGGGGTTc                                                  <  2:399329/138‑1 (MQ=255)                                                    aGCTGAGTGTGTAGCGGGTTAATTCGGCGTTTAAGCCCTGGCGACTGCTGGCATTGAGCACGCCGAGCAGGGTTCCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGCCAGCGTCGAGCTGGGGTTCat                                                <  1:29363/139‑1 (MQ=255)                                                       tGAGTGTGTAGCGGGTTAATTCGGCGTTTAAGCCCTGGCGACTGCTGGCATTGAGCACGCCGAGCAGGGTTCCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGCCAGCGTCGAGCTGGGGTTCatat                                              >  2:97266/1‑138 (MQ=255)                                                               tAGCGGGTTAATTCGGCGTTTAAGCCCTGGCGACTGCTGGCATTGAGCACGCCGAGCAGGGTTCCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGCCAGCGTCGAGCTGGGGTTCATATCAATAATAc                                     >  2:259040/1‑139 (MQ=255)                                                                 gCGGGTTAATTCGGCGTTTAAGCCCTGGCGACTGCTGGCTTTGAGCACCCCGAGCAGGGTTCCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGCCAGCGTCGAGCTGGGGTTCATATCAATAATACTg                                   <  2:326499/139‑1 (MQ=255)                                                                   gggTTAATTCGGCGTTTAAGCCCTGGCGACTGCTGGCATTGAGCACGCCGAGCAGGGTTCCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGCCAGCGTCGAGCTGGGGTTCATATCAATAATACTGtt                                 >  2:32977/1‑139 (MQ=255)                                                                     gTTAATTCGGCGTTTAAGCCCTGGCGCCTGCTGGCATTGAGCACGCCGAGCAGGGTTCCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGCCAGCGTCGAGCTGGGGTTCATATCAATAATACTGTtga                               <  1:147323/139‑1 (MQ=255)                                                                        aaTTCGGCGTTTAAGCCCTGGCGACTGCTGGCATTGAGCACGCCGAGCAGGGTTCCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGCCAGCGTCGAGCTGGGGTTCATATCAATAATACTGTtgagt                             <  1:259040/138‑1 (MQ=255)                                                                         aTTCGGCGTTTAAGCCCTGGCGACTGCTGGCATTGAGCACGCCGAGCAGGGTTCCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGCCAGCGTCGAGCTGGGGTTCATATCAATAATACTGTtgagt                             >  2:290932/1‑137 (MQ=255)                                                                                                  gctgGCATTGAGCACGCCGAGCAGGGTTCCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGCCAGCGTCGAGCTGGGGTTCATATCAATAATACTGTTGAGTGAGACGTGTAGCGCATCGGCATCACaa  >  2:57711/1‑139 (MQ=255)                                                                                                                              |                                                                                                               GAGTGTCGAGCGCGCCTTTCGCTGAGGAGAGTTTGCGCTCAAGCACCATCAAGCTGAGTGTGTAGCGGGTTAATTCGGCGTTTAAGCCCTGGCGACTGCTGGCATTGAGCACGCCGAGCAGGGTTTCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGCCAGCGTCGAGCTGGGGTTCATATCAATAATACTGTTGAGTGAGACGTGTAGCGCATCGGCATCACAA  >  NZ_CP009273/1187763‑1187998

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑