Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	4,629,926	C→T	A66A (GCG→GCA)	arcA ←	two‑component system response regulator ArcA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	4,629,926	0	C	T	100.0%	140.9 / NA	35	A66A (GCG→GCA)	arcA	two‑component system response regulator ArcA
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (18/17);  total (18/17)

TCGTCAGTTCACGCGGGTTGAACGGTTTGGTGATGTAGTCATCTGCACCGATTTCGAGGCCGAGAATTTTATCGACTTCGTTGTCACGGCCAGTCAGGAACATCAACGCAACATTCGCCTGCTCGCGCAGTTCACGCGCTAACAGAAGACCGTTCTTACCCGGCAGATTGATATCCATGATCACCAGGTTGATGTCATATTCAGAGAGGATCTGATGCATTTCCGCGCCATCTGTCGCTTCGAAAACATCATAGCCTTCC  >  NZ_CP009273/4629790‑4630049                                                                                                                                         |                                                                                                                            tCGTCAGTTCACGCGGGTTGAACGGTTTGGTGATGTAGTCATCTGCACCGATTTCGAGGCCGAGAATTTTATCGACTTCGTTGTCACGGCCAGTCAGGAACATCAACGCAACATTCGCCTGCTCGCGCAGTTCACgtgc                                                                                                                           <  2:228498/139‑1 (MQ=255)           aCGCGGGTTGAACGGTTTGGTGATGTAGTCATCTGCACCGATTTCGAGGCCGAGAATTTTATCGACTTCGTTGTCACGGCCAGTCAGGAACATCAACGCAACATTCGCCTGCTCGCGCAGTTCACGTGCTAACagaag                                                                                                                  <  1:30452/138‑1 (MQ=255)            cgcgGGTTGAACGGTTTGGTGATGTAGTCATCTGCACCGATTTCGAGGCCGAGAATTTTATCGACTTCGTTGTCACGGCCAGTCAGGAACATCAACGCAACATTCGCCTGCTCGCGCAGTTCACGTGCTAACAGAAGAc                                                                                                                <  1:45446/139‑1 (MQ=255)                  ttGAACGGTTTGGTGATGTAGTCATCTGCACCGATTTCGAGGCCGAGAATTTTATCGACTTCGTTGTCACGGCCAGTCAGGAACATCAACGCAACATTCGCCTGCTCGCGCAGTTCACGTGCTAACAGAAGACCGTTCt                                                                                                          >  2:15109/1‑139 (MQ=255)                           ttGGTGATGTAGTCATCTGCACCGATTTCGAGGCCGAGAATTTTATCGACTTCGTTGTCACGGCCAGTCAGGAACATCAACGCAACATTCGCCTGCTCGCGCAGTTCACGTGCTAACAGAAGACCGTTCTTACCCgg                                                                                                   >  2:96377/1‑137 (MQ=255)                           ttGGTGATGTAGTCATCTGCACCGATTTCGAGGCCGAGAATTTTATCGACTTCGTTGTCACGGCCAGTCAGGAACATCAACGCAACATTCGCCTGCTCGCGCAGTTCACGTGCTAACAGAAGACCGTTCTTACCCgg                                                                                                   >  2:347589/1‑137 (MQ=255)                              gTGATGTAGTCATCTGCACCGATTTCGAGGCCGAGAATTTTATCGACTTCGTTGTCACGGCCAGTCAGGAACATCAACGCAACATTCGCCTGCTCGCGCAGTTCACGTGCTAACAGAAGACCGTTCTTACCCGGCAGa                                                                                               <  1:433807/138‑1 (MQ=255)                                    tAGTCATCTGCACCGATTTCGAGGCCGAGAATTTTATCGACTTCGTTGTCACGGCCAGTCAGGAACATCAACGCAACATTCGCCTGCTCGCGCAGTTCACGTGCTAACAGAAGACCGTTCTTACCCGGCAGAt                                                                                              >  2:130831/1‑133 (MQ=255)                                    tAGTCATCTGCACCGATTTCGAGGCCGAGAATTTTATCGACTTCGTTGTCACGGCCAGTCAGGAACATCAACGCAACATTCGCCTGCTCGCGCAGTTCACGTGCTAACAGAAGACCGTTCTTACCCGGCAGAt                                                                                              <  1:130831/133‑1 (MQ=255)                                    tAGTCATCTGCACCGATTTCGAGGCCGAGAATTTTATCGACTTCGTTGTCACGGCCAGTCAGGAACATCAACGCAACATTCGCCTGCTCGCGCAGTTCACGTGCTAACAGAAGACCGTTCTTACCCGGCAGATTGatat                                                                                        >  1:62478/1‑139 (MQ=255)                                    tAGTCATCTGCACCGATTTCGAGGCCGAGAATTTTATCGACTTCGTTGTCACGGCCAGTCAGGAACATCAACGCAACATTCGCCTGCTCGCGCAGTTCACGTGCTAACAGAAGACCGTTCTTACCCGGCAGATTGatat                                                                                        >  2:359436/1‑139 (MQ=255)                                        cATCTGCACCGATTTCGAGGCCGAGAATTTTATCGACTTCGTTGTCACGGCCAGTCAGGAACATCAACGCAACATTCGCCTGCTCGCGCAGTTCACGTGCTAACAGAAGACCGTTCTTACCCGGCAGATTGATATCCAt                                                                                    >  2:75643/1‑139 (MQ=255)                                        cATCTGCACCGATTTCGAGGCCGAGAATTTTATCGACTTCGTTGTCACGGCCAGTCAGGAACATCAACGCAACATTCGCCTGCTCGCGCAGTTCACGTGCTAACAGAAGACCGTTCTTACCCGGCAGATTGATATCCAt                                                                                    >  1:248078/1‑139 (MQ=255)                                         aTCTGCACCGATTTCGAGGCCGAGAATTTTATCGACTTCGTTGTCACGGCCAGTCAGGAACATCAACGCAACATTCGCCTGCTCGCGCAGTTCACGTGCTAACAGAAGACCGTTCTTACCCGGCAg                                                                                                >  2:147094/1‑126 (MQ=255)                                         aTCTGCACCGATTTCGAGGCCGAGAATTTTATCGACTTCGTTGTCACGGCCAGTCAGGAACATCAACGCAACATTCGCCTGCTCGCGCAGTTCACGTGCTAACAGAAGACCGTTCTTACCCGGCAg                                                                                                <  1:147094/126‑1 (MQ=255)                                            tGCACCGATTTCGAGGCCGAGAATTTTATCGACTTCGTTGTCACGGCCAGTCAGGAACATCAACGCAACATTCGCCTGCTCGCGCAGTTCACGTGCTAACAGAAGACCGTTCTTACCCGGCAGATTGATATCCATGAt                                                                                 >  2:367160/1‑138 (MQ=255)                                                 cGATTTCGAGGCCGAGAATTTTATCGACTTCGTTGTCACGGCCAGTCAGGAACATCAACGCAACATTCGCCTGCTCGCGCAGTTCACGTGCTAACAGAAGACCGTTCTTACCCGGCAGATTGATATCCATGATCACCAg                                                                           >  1:56925/1‑139 (MQ=255)                                                 cGATTTCGAGGCCGAGAATTTTATCGACTTCGTTGTCACGGCCAGTCAGGAACATCAACGCAACATTCGCCTGCTCGCGCAGTTCACGTGCTAACAGAAGACCGTTCTTACCCGGCAGATTGATATCCATGATCACCAg                                                                           >  2:109656/1‑139 (MQ=255)                                                  gATTTCGAGGCCGAGAATTTTATCGACTTCGTTGTCACGGCCAGTCAGGAACATCAACGCAACATTCGCCTGCTCGCGCAGTTCACGTGCTAACAGAAGACCGTTCTTACCCGGCAGATTGATATCCATGATCACCAgg                                                                          <  1:142985/139‑1 (MQ=255)                                                   aTTTCGAGGCCGAGAATTTTATCGACTTCGTTGTCACGGCCAGTCAGGAACATCAACGCAACATTCGCCTGCTCGCGCAGTTCACGTGCTAACAGAAGACCGTTCTTACCCGGCAGATTGATATCCATGATCACCAGGt                                                                         <  1:420372/139‑1 (MQ=255)                                                   aTTTCGAGGCCGAGAATTTTATCGACTTCGTTGTCACGGCCAGTCAGGAACATCAACGCAACATTCGCCTGCTCGCGCAGTTCACGTGCTAACAGAAGACCGTTCTTACCCGGCAGATTGATATCCATGATCACCAGGt                                                                         >  1:255072/1‑139 (MQ=255)                                                   aTTTCGAGGCCGAGAATTTTATCGACTTCGTTGTCACGGCCAGTCAGGAACATCAACGCAACATTCGCCTGCTCGCGCAGTTCACGTGCTAACAGAAGACCGTTCTTACCCGGCAGATTGATATCCATGATCACCAGGt                                                                         >  2:294962/1‑139 (MQ=255)                                                        gAGGCCGAGAATTTTATCGACTTCGTTGTCACGGCCAGTCAGGAACATCAACGCAACATTCGCCTGCTCGCGCAGTTCACGTGCTAACAGAAGACCGTTCTTACCCGGCAGATTGATATCCATGATCACCAGGTTGATg                                                                    <  1:368128/139‑1 (MQ=255)                                                          ggCCGAGAATTTTATCGACTTCGTTGTCACGGCCAGTCAGGAACATCAACGCAACATTCGCCTGCTCGCGCAGTTCACGTGCTAACAGAAGACCGTTCTTACCCGGCAGATTGATATCCATGATCACCAGGTTGATGTc                                                                  <  1:352301/139‑1 (MQ=255)                                                                  aTTTTATCGACTTCGTTGTCACGGCCAGTCAGGAACATCAACGCAACATTCGCCTGCTCGCGCAGTTCACGTGCTAACAGAAGACCGTTCTTACCCGGCAGATTGATATCCATGATCACCAGGTTGATGTCATATTCag                                                          <  1:256791/139‑1 (MQ=255)                                                                     ttATCGACTTCGTTGTCACGGCCAGTCAGGAACATCAACGCAACATTCGCCTGCTCGCGCAGTTCACGTGCTAACAGAAGACCGTTCTTACCCGGCAGATTGATATCCATGATCACCAGGTTGATGTCATATTCagag                                                        <  2:132528/138‑1 (MQ=255)                                                                     ttATCGACTTCGTTGTCACGGCCAGTCAGGAACATCAACGCAACATTCGCCTGCTCGCGCAGTTCACGTGCTAACAGAAGACCGTTCTTACCCGGCAGATTGATATCCATGATCACCAGGTTGATGTCATATTCagag                                                        <  2:62478/138‑1 (MQ=255)                                                                     ttATCGACTTCGTTGTCACGGCCAGTCAGGAACATCAACGCAACATTCGCCTGCTCGCGCAGTTCACGTGCTAACAGAAGACCGTTCTTACCCGGCAGATTGATATCCATGATCACCAGGTTGATGTCATATTCagag                                                        <  1:89952/138‑1 (MQ=255)                                                                      tATCGACTTCGTTGTCACGGCCAGTCAGGAACATCAACGCAACATTCGCCTGCTCGCGCAGTTCACGTGCTAACAGAAGACCGTTCTTACCCGGCAGATTGATATCCATGATCACCAGGTTGATGTCATATTCagaga                                                       <  1:131610/138‑1 (MQ=255)                                                                       aTCGACTTCGTTGTCACGGCCAGTCAGGAACATCAACGCAACATTCGCCTGCTCGCGCAGTTCACGTGCTAACAGAAGACCGTTCTTACCCGGCAGATTGATATCCATGATCACCAGGTTGATGTCATATTCagagag                                                      <  1:187422/138‑1 (MQ=255)                                                                                              tCAGGAACATCAACGCAACATTCGCCTGCTCGCGCAGTTCACGTGCTAACAGAAGACCGTTCTTACCCGGCAGATTGATATCCATGATCACCAGGTTGATGTCATATTCAGAGAGGATCTGATGCATTTCCGCGCCATc                              >  1:417194/1‑139 (MQ=255)                                                                                                        cAACGCAACATTCGCCTGCTCGCGCAGTTCACGTGCTAACAGAAGACCGTTCTTACCCGGCAGATTGATATCCATGATCACCAGGTTGATGTCATATTCAGAGAGGATCTGATg                                             <  2:210023/114‑1 (MQ=255)                                                                                                        cAACGCAACATTCGCCTGCTCGCGCAGTTCACGTGCTAACAGAAGACCGTTCTTACCCGGCAGATTGATATCCATGATCACCAGGTTGATGTCATATTCAGAGAGGATCTGATg                                             >  1:210023/1‑114 (MQ=255)                                                                                                                 aTTCGCCTGCTCGCGCAGTTCACGTGCTAACAGAAGACCGTTCTTACCCGGCAGATTGATATCCATGATCACCAGGTTGATGTCATATTCAGAGAGGATCTGATGCATTTCCGCGCCATCTGTCGCTTCGAAAAcatca           <  1:294962/139‑1 (MQ=255)                                                                                                                     gCCTGCTCGCGCAGTTCACGTGCTAACAGAAGACCGTTCTTACCCGGCAGATTGATATCCATGATCACCAGGTTGATGTCATATTCAGAGAGGATCTGATGCATTTCCGCGCCATCTGTCGCTTCGAAAACATCATAGc       >  2:22363/1‑139 (MQ=255)                                                                                                                          cTCGCGCAGTTCACGTGCTAACAGAAGACCGTTCTTACCCGGCAGATTGATATCCATGATCACCAGGTTGATGTCATATTCAGAGAGGATCTGATGCATTTCCGCGCCATCTGTCGCTTCGAAAACATCATAGCCTTcc  >  2:116867/1‑139 (MQ=255)                                                                                                                                         |                                                                                                                            TCGTCAGTTCACGCGGGTTGAACGGTTTGGTGATGTAGTCATCTGCACCGATTTCGAGGCCGAGAATTTTATCGACTTCGTTGTCACGGCCAGTCAGGAACATCAACGCAACATTCGCCTGCTCGCGCAGTTCACGCGCTAACAGAAGACCGTTCTTACCCGGCAGATTGATATCCATGATCACCAGGTTGATGTCATATTCAGAGAGGATCTGATGCATTTCCGCGCCATCTGTCGCTTCGAAAACATCATAGCCTTCC  >  NZ_CP009273/4629790‑4630049

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑