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%	69.2 / NA	21	E67G (GAA→GGA)	hflD	high frequency lysogenization protein HflD
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (9/12);  total (9/12)

TCGAGCGCGCCTTTCGCTGAGGAGAGTTTGCGCTCAAGCACCATCAAGCTGAGTGTGTAGCGGGTTAATTCGGCGTTTAAGCCCTGGCGACTGCTGGCATTGAGCACGCCGAGCAGGGTTTCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGCCAGCGTCGAGCTGGGGTTCATATCAATAATACTGTTGAGTGAGACGTGTAGCGCATCGGCATCACAATGCCCCTGGTGAGCG  >  NZ_CP009273/1187768‑1188013                                                                                                                         |                                                                                                                              tCGAGCGCGCCTTTCGCTGAGGAGAGTTTGCGCTCAAGCACCATCAAGCTGAGTGTGTAGCGGGTTAATTCGGCGTTTAAGCCCTGGCGACTGCTGGCATTGAGCACGCCGAGCAGGGTTCCCAGCCCGACGCGCAgg                                                                                                              <  2:180107/138‑1 (MQ=255)         gcCTTTCGCTGAGGAGAGTTTGCGCTCAAGCACCATCAAGCTGAGTGTGTAGCGGGTTAATTCGGCGTTTAAGCCCTGGCGACTGCTGGCATTGAGCACGCCGAGCAGGGTTCCCAGCCCGACGCGCAGGTTGGCTTCg                                                                                                     <  1:313840/139‑1 (MQ=255)                     ggagAGTTTGCGCTCAAGCACCATCAAGCTGAGTGTGTAGCGGGTTAATTCGGCGTTTAAGCCCTGGCGACTGCTGGCATTGAGCACGCCGAGCAGGGTTCCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCaaa                                                                                          >  2:292417/1‑138 (MQ=255)                              gcgcTCAAGCACCATCAAGCTGAGTGTGTAGCGGGTTAATTCGGCGTTTAAGCCCTGGCGACTGCTGGCATTGAGCACGCCGAGCAGGGTTCCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGCCAGc                                                                                >  2:451256/1‑139 (MQ=255)                                 cTCAAGCACCATCAAGCTGAGTGTGTAGCGGGTTAATTCGGCGTTTAAGCCCTGGCGACTGCTGGCATTGAGCACGCCGAGCAGGGTTCCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGCCAGCGTc                                                                             >  1:175178/1‑139 (MQ=255)                                       cACCATCAAGCTGAGTGTGTAGCGGGTTAATTCGGCGTTTAAGCCCTGGCGACTGCTGGCATTGAGCACGCCGAGCAGGGTTCCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGCCAGCGTCGAGCTg                                                                       <  1:44832/139‑1 (MQ=255)                                                    aGTGTGTAGCGGGTTAATTCGGCGTTTAAGCCCTGGCGACTGCTGGCATTGAGCACGCCGAGCAGGGTTCCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGCCAGCGTCGAGCTGGGGTTCATATCaa                                                          >  1:389374/1‑139 (MQ=255)                                                    aGTGTGTAGCGGGTTAATTCGGCGTTTAAGCCCTGGCGACTGCTGGCATTGAGCACGCCGAGCAGGGTTCCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGCCAGCGTCGAGCTGGGGTTCATATCaa                                                          <  2:175178/139‑1 (MQ=255)                                                          tAGCGGGTTAATTCGGCGTTTAAGCCCTGGCGACTGCTGGCATTGAGCACGCCGAGCAGGGTTCCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGCCAGCGTCGAGCTgggg                                                                    >  1:242971/1‑123 (MQ=255)                                                          tAGCGGGTTAATTCGGCGTTTAAGCCCTGGCGACTGCTGGCATTGAGCACGCCGAGCAGGGTTCCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGCCAGCGTCGAGCTgggg                                                                    <  2:242971/123‑1 (MQ=255)                                                                tttAATTCGGCGTTTAAGCCCTGGCGACTGCTGGCATTGAGCACGCCGAGCAGGGTTCCCAGCCCGACGCGCAGGTTGGCTCCGCTACCGCCAAAAACCGCCAGCg                                                                               <  2:30079/105‑1 (MQ=255)                                                                gTTAATTCGGCGTTTAAGCCCTGGCGCCTGCGGGCATTGAGCACGCCGAGCAGGGTTCCCAGCCCGACGCGCAGGTTGGCTTCGCTCCCGCCAAAAACCGCCAGCGTCGAGCTGGGGTTCATATCAATAATACTGTtga                                              <  2:127116/139‑1 (MQ=255)                                                                gTTAATTCGGCGTTTAAGCCCTGGCGACTGCTGGCATTGAGCACGCCGAGCAGGGTTCCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGCCAGCg                                                                               >  1:30079/1‑106 (MQ=255)                                                                gTTAATTCGGCGTTTAAGCCCTGGCGACTGCTGGCATTGAGCACGCCGAGCAGGGTTCCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGCCAGCGTCGAGCTGGGGTTCat                                                               >  2:4717/1‑122 (MQ=255)                                                                gTTAATTCGGCGTTTAAGCCCTGGCGACTGCTGGCATTGAGCACGCCGAGCAGGGTTCCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGCCAGCGTCGAGCTGGGGTTCat                                                               <  1:4717/122‑1 (MQ=255)                                                                  tAATTCGGCGTTTAAGCCCTGGCGACTGCTGGCATTGAGCACGCCGAGCAGGGTTCCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGCCAGCGTCGAGCTGGGGTTCATATCAATAATACTGTtgagt                                            >  2:513093/1‑139 (MQ=255)                                                                   attccGGCGTTTAGGCCCTGGCGGCTGCGGGCATTGAGGACGCCGAGCAGGGTTCCCCGCCCGACGCGCAGGTTGGCTTCGCTACCGCCAAAACCCGCCAGCGTCGAGCTGGGGTTCATATCAATAATACTGTtgagt                                            <  1:465160/134‑1 (MQ=255)                                                                   aaTTCGGCGTTTAAGCCCTGGCGACTGCTGGCATTGAGCACGCCGAGCAGGGTTCCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGCCAGCGTCGAGCTGGGGTTCATATCAATAATACTGTtgagt                                            <  1:492792/138‑1 (MQ=255)                                                                                       gCGACTGCTGGCATTGAGCACGCCGAGCAGGGTTCCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGCCAGCGTCGAGCTGGGGTTCATATCAATAATACTGTTGAGTGAGACGTGTAGCGCATCGGCa                       >  2:511044/1‑139 (MQ=255)                                                                                              ctgGCATTGAGCACGCCGAGCAGGGTTCCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGCCAGCGTCGAGCTGGGGTTCATATCAATAATACTGTTGAGTGAGACGTGTAGCGCATCGGCATCACaa                 <  1:292417/138‑1 (MQ=255)                                                                                                            gCCGAGCGGGGTTCCCAGCCCGCCGCGCAGGTTGGCTTCGCTCCCGCCAAAAACCGCCAGCGTCGAGCTGGGGTTCATATCAATAATACTGTTGAGTGAGACGTGTAGCGCATCGGCATCACAATGCCCCTGGTGAGCg  <  1:355918/139‑1 (MQ=255)                                                                                                                         |                                                                                                                              TCGAGCGCGCCTTTCGCTGAGGAGAGTTTGCGCTCAAGCACCATCAAGCTGAGTGTGTAGCGGGTTAATTCGGCGTTTAAGCCCTGGCGACTGCTGGCATTGAGCACGCCGAGCAGGGTTTCCAGCCCGACGCGCAGGTTGGCTTCGCTACCGCCAAAAACCGCCAGCGTCGAGCTGGGGTTCATATCAATAATACTGTTGAGTGAGACGTGTAGCGCATCGGCATCACAATGCCCCTGGTGAGCG  >  NZ_CP009273/1187768‑1188013

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑