Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	3,649,376	(T)5→4	coding (277/327 nt)	hdeB ←	acid‑activated periplasmic chaperone HdeB

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,649,372	0	T	.	100.0%	110.1 / NA	26	coding (281/327 nt)	hdeB	acid‑activated periplasmic chaperone HdeB
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base . (12/14);  total (12/14)

CAACTTGCTACTCCTTTTTACTTGCACCTCATTAATTCGGCAAGTCATTAGATGCTTGATTTTTGAAGGTATACAAATTTTTCTGCGGGTTTTTCTTACAGTATTCGATCACTTTAGGAATTTGAGTGAGATCGGTTTCATTTAAAGTAACGGTATCGCCAC  >  NZ_CP009273/3649295‑3649456                                                                              |                                                                                     cAACTTGCTACTCCTTTTTACTTGCACCTCATTAATTCGGCAAGTCATTAGATGCTTGATTTTTGAAGGTATACAAA‑TTTTCTGCGGGtt                                                                         <  1:449074/90‑1 (MQ=255) cAACTTGATAGTCCTGTTTACTTGCACCTCATAAATTCGGCAAGTCATTAGATGATTGATTTTTAAAGGTATACAAA‑TTTTCTGCGGGtt                                                                         <  1:398719/90‑1 (MQ=255)        cTACTCCTTTTTACTTGCACCTCATTAATTCGGCAAGTCATTAGATGCTTGATTTTTGAAGGTATACAAA‑TTTTCTGCGGGTTTTTCTTa                                                                  >  2:372777/1‑90 (MQ=255)         tACTCCTTTTTACTTGCACCTCATTAATTCGGCAAGTCATTAGATGCTTGATTTTTGAAGGTATACAAA‑TTTTCTGCGGGTTTTTCTTAc                                                                 <  2:226263/90‑1 (MQ=255)                ttttACTTGCACCTCATTAATTCGGCAAGTCATTAGATGCTTGATTTTTGAAGGTATACAAA‑TTTTCTGCGGGTTTTTCTTACAGTATTc                                                          >  2:151605/1‑90 (MQ=255)                ttttACTTGCACCTCATTAATTCGGCAAGTCATTAGATGCTTGATTTTTGAAGGTATACAAA‑TTTTCTGCGGGTTTTTCTTACAGTATTc                                                          >  1:547534/1‑90 (MQ=255)                    aCTTGCACCTCATTAATTCGGCAAGTCATTAGATGCTTGATTTTTGAAGGTATACAAA‑TTTTCTGCGGGTTTTTCTTACAGTATTCGATc                                                      <  1:506841/90‑1 (MQ=255)                       tGCACCTCATTAATTCGGCAAGTCATTAGATGCTTGATTTTTGAAGGTATACAAA‑TTTTCTGCGGGTTTTTCTTACAGTATTCGATCACt                                                   >  2:326371/1‑90 (MQ=255)                       tGCACCTCATTAATTCGGCAAGTCATTAGATGCTTGATTTTTGAAGGTATACAAA‑TTTTCTGCGGGTTTTTCTTACAGTATTCGATCACt                                                   >  2:188809/1‑90 (MQ=255)                       tGCACCTCATTAATTCGGCAAGTCATTAGATGCTTGATTTTTGAAGGTATACAAA‑TTTTCTGCGGGTTTTTCTTACAGTATTCGATCACt                                                   >  1:342484/1‑90 (MQ=255)                       tGCACCTCATTAATTCGGCAAGTCATTAGATGCTTGATTTTTGAAGGTATACAAA‑TTTTCTGCGGGTTTTTCTTACAGTATTCGATCACt                                                   >  1:350972/1‑90 (MQ=255)                            cTCATTAATTCGGCAAGTCATTAGATGCTTGATTTTTGAAGGTATACAAA‑TTTTCTGCGGGTTTTTCTTACAGTATTCGATCACTTTAgg                                              <  1:298759/90‑1 (MQ=255)                                        gCAAGTCATTAGATGCTTGATTTTTGAAGGTATACAAA‑TTTTCTGCGGGTTTTTCTTACAGTATTCGATCACTTTAGGAATTtgagtgag                                  >  2:613835/1‑90 (MQ=255)                                        gCAAGTCATTAGATGCTTGATTTTTGAAGGTATACAAA‑TTTTCTGCGGGTTTTTCTTACAGTATTCGATCACTTTAGGAATTtgagtgag                                  >  1:253218/1‑90 (MQ=255)                                               aTTAGATGCTTGATTTTTGAAGGTATACAAA‑TTTTCTGCGGGTTTTTCTTACAGTATTCGATCACTTTAGGAATTTGAGTGAGATCGGtt                           <  1:77978/90‑1 (MQ=255)                                               aTTAGATGCTTGATTTTTGAAGGTATACAAA‑TTTTCTGCGGGTTTTTCTTACAGTATTCGATCACTTTAGGAATTTGAGTGAGATCGGtt                           <  2:454231/90‑1 (MQ=255)                                                ttAGATGCTTGATTTTTGAAGGTATACAAA‑TTTTCTGCGGGTTTTTCTTACAGTATTCGATc                                                      >  2:204838/1‑62 (MQ=255)                                                ttAGATGCTTGATTTTTGAAGGTATACAAA‑TTTTCTGCGGGTTTTTCTTACAGTATTCGATc                                                      <  1:204838/62‑1 (MQ=255)                                                       cTTGATTTTTGAAGGTATACAAA‑TTTTCTGCGGGTTTTTCTTACAGTATTCGATCACTTTAGGAATTTGAGTGAGATCGGTTTCATTTaa                   <  1:293168/90‑1 (MQ=255)                                                        ttGATTTTTGAAGGTATACAAA‑TTTTCTGCGGGTTTTTCTTACAGTATTCGATCACTTTAGGAATTTGAGTGAGATCGGTTTCATTTaaa                  >  2:394809/1‑90 (MQ=255)                                                                     gTATACAAA‑TTTTCTGCGGGTTTTTCTTACAGTATTCGATCACTTTAGGAATTTGAGTGAGATCGGTTTCATTTAAAGTAACGGTATCGc     >  1:472202/1‑90 (MQ=255)                                                                      tataCAAA‑TTTTCTGCGGGTTTTTCTTACAGTATTCGATCACTTTAGGAATTTGAGTGAGATCGGTTTCATTTAAAGTAACGGTATCGcc    <  1:394809/90‑1 (MQ=255)                                                                      tataCAAA‑TTTTCTGCGGGTTTTTCTTACAGTATTCGATCACTTTAGGAATTTGAGTGAGATCGGTTTCATTTAAAGTAACGGTATCGcc    <  1:326371/90‑1 (MQ=255)                                                                        taCAAA‑TTTTCTGCGGGTTTTTCTTACAGTATTCGATCACTTTAGGAATTTGAGTGAGATCGGTTTCATTTAAAGTAACGGTATCGCCAc  <  2:122002/90‑1 (MQ=255)                                                                        taCAAA‑TTTTCTGCGGGTTTTTCTTACAGTATTCGATCACTTTAGGAATTTGAGTGAGATCGGTTTCATTTAAAGTAACGGTATCGCCAc  <  1:222044/90‑1 (MQ=255)                                                                        taCAAA‑TTTTCTGCGGGTTTTTCTTACAGTATTCGATCACTTTAGGAATTTGAGTGAGATCGGTTTCATTTAAAGTAACGGTATCGCCAc  <  2:603237/90‑1 (MQ=255)                                                                              |                                                                                     CAACTTGCTACTCCTTTTTACTTGCACCTCATTAATTCGGCAAGTCATTAGATGCTTGATTTTTGAAGGTATACAAATTTTTCTGCGGGTTTTTCTTACAGTATTCGATCACTTTAGGAATTTGAGTGAGATCGGTTTCATTTAAAGTAACGGTATCGCCAC  >  NZ_CP009273/3649295‑3649456

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑