Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	3,650,010	(T)6→5	coding (91/333 nt)	hdeA ←	acid‑activated periplasmic chaperone HdeA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,650,005	0	T	.	100.0%	136.6 / NA	32	coding (96/333 nt)	hdeA	acid‑activated periplasmic chaperone HdeA
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base . (14/18);  total (14/18)

GCGCTTCAGCAAAACCAACTGCAGTTGGCTGGAAGGATTCGTCCACAGCCAGGAAATCTTCACAGGTCCAGGAGTTGACCGGTTTTTTGTTATCAGCTGCTTTTTGCGCATCCGCTGCATTGCTCACAACTGGCAGAAGAAGCAGACCACCAAGAATAACGCCTAA  >  NZ_CP009273/3649923‑3650088                                                                                   |                                                                                    gcgcTTCAGCAAAACCAACTGCAGTTGGCTGGAAGGATTCGTCCACAGCCAGGAAATCTTCACAGGTCCAGGAGTTGACCGGtttttgtt                                                                              >  1:121129/1‑87 (MQ=255)  cgcTTCAGCAAAACCAACTGCAGTTGGCTGGAAGGATTCGTCCACAGCCAGGAAATCTTCACAGGTCCAGGAGTTGACCGGtttttgtta                                                                             <  2:179329/90‑5 (MQ=255)      tCAGCAAAACCAACTGCAGTTGGCTGGAAGGATTCGTCCACAGCCAGGAAATCTTCACAGGTCCAGGAGTTGACCGG‑TTTTTGTTATCAg                                                                        >  1:270369/1‑90 (MQ=255)      tCAGCAAAACCAACTGCAGTTGGCTGGAAGGATTCGTCCACAGCCAGGAAATCTTCACAGGTCCAGGAGTTGACCGG‑TTTTTGTTATCAg                                                                        <  2:509930/90‑1 (MQ=255)        aGCAAAACCAACTGCAGTTGGCTGGAAGGATTCGTCCACAGCCAGGAAATCTTCACAGGTCCAGGAGTTGACCGG‑TTTTTGTTATCAgct                                                                      <  1:422332/90‑1 (MQ=255)                   cTGCAGTTGGCTGGAAGGATTCGTCCACAGCCAGGAAATCTTCACAGGTCCAGGAGTTGACCGG‑TTTTTGTTATCAGCTGCTTTTTgcgc                                                           >  1:210563/1‑90 (MQ=255)                    tGCAGTTGGCTGGAAGGATTCGTCCACAGCCAGGAAATCTTCACAGGTCCAGGAGTTGACCGG‑TTTTTGTTATCAGCTGCTTTTTGCGCa                                                          <  2:210563/90‑1 (MQ=255)                       aGTTGGCTGGAAGGATTCGTCCACAGCCAGGAAATCTTCACAGGTCCAGGAGTTGACCGG‑TTTTTGTTATCAGCTGCTTTTTGCGCATcc                                                       <  2:162969/90‑1 (MQ=255)                             cTGGAAGGATTCGTCCACAGCCAGGAAATCTTCACAGGTCCAGGAGTTGACCGG‑TTTTTGTTATCAGCTGCTTTTTGCGCATCCGCTGCa                                                 >  2:254908/1‑90 (MQ=255)                              tGGAAGGATTCGTCCACAGCCAGGAAATCTTCACAGGTCCAGGAGTTGACCGG‑TTTTTGTTATCAGCTGCTTTTTGCGCATCCGCTGCAt                                                <  2:547155/90‑1 (MQ=255)                              tGGAAGGATTCGTCCACAGCCAGGAAATCTTCACAGGTCCAGGAGTTGACCGG‑TTTTTGTTATCAGCTGCTTTTTGCGCATCCGCTGCAt                                                <  2:287170/90‑1 (MQ=255)                              tGGAAGGACTCGTCCACAGCCAGGAAATCTTCACAGGTCCAGGAGTTGACCGG‑TTTTTGTTATCAGCTGCTTTTTGCGCATCCGCTGCAt                                                <  1:24357/90‑1 (MQ=255)                                   ggATTCGTCCACAGCCAGGAAATCTTCACAGGTCCAGGAGTTGACCGG‑TTTTTGTTATCAGCTGCTTTTTGCGCATCCGCTGCATTGCTc                                           <  2:533521/90‑1 (MQ=255)                                   ggATTCGTCCACAGCCAGGAAATCTTCACAGGTCCAGGAGTTGACCGG‑TTTTTGTTATCAGCTGCTTTTTGCGCATCCGCTGCATTGCTc                                           <  2:270369/90‑1 (MQ=255)                                     aTTCGTCCACAGCCAGGAAATCTTCACAGGTCCAGGAGTTGACCGG‑TTTTTGTTATCAGCTGCTTTTTGCGCATCCGCTGCATTGCTcac                                         <  2:85550/90‑1 (MQ=255)                                              caGCCAGGAAATCTTCACAGGTCCAGGAGTTGACCGG‑TTTTTGTTATCAGCTGCTTTTTGCGCATCCGCTGCATTGCTCACAACTGGCag                                >  1:338905/1‑90 (MQ=255)                                                   aGGAAATCTTCACAGGTCCAGGAGTTGACCGG‑TTTTTGTTATCAGCTGCTTTTTGCGCATCCGCTGCAt                                                <  2:557956/69‑1 (MQ=255)                                                   aGGAAATCTTCACAGGTCCAGGAGTTGACCGG‑TTTTTGTTATCAGCTGCTTTTTGCGCATCCGCTGCAt                                                >  1:557956/1‑69 (MQ=255)                                                   aGGAAATCTTCACAGGTCCAGGAGTTGACCGG‑TTTTTGTTATCAGCTGCTTTTTGCGCATCCGCTGCATTGCTCACAACTGGCAgaagaa                           >  2:117601/1‑90 (MQ=255)                                                         tCTTCACAGGTCCAGGAGTTGACCGG‑TTTTTGTTATCAGCTGCTTTTTGCGCATCCGCTGCATTGCTCACAACTGGCAGAAGAAGCAGac                     <  2:282203/90‑1 (MQ=255)                                                              acaGGTCCAGGAGTTGACCGG‑TTTTTGTTATCAGCTGCTTTTTGCGCATCCGCTGCATTGCTCACAACTGGCAGAAGAAGCAGAccacca                <  1:89275/90‑1 (MQ=255)                                                              acaGGTCCAGGAGTTGACCGG‑TTTTTGTTATCAGCTGCTTTTTGCGCATCCGCTGCATTGCTCACAACTGGCAGAAGAAGCAGAccacca                <  2:192802/90‑1 (MQ=255)                                                                       ggAGTTGACCGG‑TTTTTGTTATCAGCTGCTTTTTGCGCATCCGCTGCATTGCTCACAACTGGCAGAAGAAGCAGACCACCAAGAATAACg       <  2:338905/90‑1 (MQ=255)                                                                         aGTTGACCGG‑TTTTTGTTATCAGCTGCTTTTTGCGCATCCGCTGCATTGCTCACAACTGGCAGAAGAAGCAGACCACCAAGAATAACGcc     >  1:491911/1‑90 (MQ=255)                                                                           ttGACCGG‑TTTTTGTTATCAGCTGCTTTTTGCGCATCCGCTGCATTGCTca                                          <  2:267354/51‑1 (MQ=255)                                                                           ttGACCGG‑TTTTTGTTATCAGCTGCTTTTTGCGCATCCGCTGCATTGCTca                                          >  1:267354/1‑51 (MQ=255)                                                                            tGACCGG‑TTTTTGTTATCAGCTGCTTTTTGCGCATCCGCTGCATTGCTCACAACTgg                                   >  1:76032/1‑57 (MQ=255)                                                                            tGACCGG‑TTTTTGTTATCAGCTGCTTTTTGCGCATCCGCTGCATTGCTCACAACTgg                                   <  2:76032/57‑1 (MQ=255)                                                                            tGACCGG‑TTTTTGTTATCAGCTGCTTTTTGCGCATCCGCTGCATTGCTCACAACTGGCaga                               <  2:389168/61‑1 (MQ=255)                                                                            tGACCGG‑TTTTTGTTATCAGCTGCTTTTTGCGCATCCGCTGCATTGCTCACAACTGGCaga                               >  1:389168/1‑61 (MQ=255)                                                                            tGACCGG‑TTTTTGTTATCAGCTGCTTTTTGCGCATCCGCTGCATTGCTCACAACTGGCAGAAGAAGCAGACCACCAAGAATAACGCCTaa  >  2:161655/1‑90 (MQ=255)                                                                            tGACCGG‑TTTTTGTTATCAGCTGCTTTTTGCGCATCCGCTGCATTGCTCACAACTGGCAGAAGAAGCAGACCACCAAGAATAACGCCTaa  >  2:299869/1‑90 (MQ=255)                                                                            tGACCGG‑TTTTTGTTATCAGCTGCTTTTTGCGCATCCGCTGCATTGCTCACAACTGGCAGAAGAAGCAGACCACCAAGAATAACGCCTaa  >  1:84212/1‑90 (MQ=255)                                                                            tGACCGG‑TTTTTGTTATCAGCTGCTTTTTGCGCATCCGCTGCATTGCTCACAACTGGCAGAAGAAGCAGACCACCAAGAATAACGCCTaa  >  1:17592/1‑90 (MQ=255)                                                                                   |                                                                                    GCGCTTCAGCAAAACCAACTGCAGTTGGCTGGAAGGATTCGTCCACAGCCAGGAAATCTTCACAGGTCCAGGAGTTGACCGGTTTTTTGTTATCAGCTGCTTTTTGCGCATCCGCTGCATTGCTCACAACTGGCAGAAGAAGCAGACCACCAAGAATAACGCCTAA  >  NZ_CP009273/3649923‑3650088

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑