Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	4,630,135	A→G	intergenic (‑12/‑84)	arcA ← / → BW25113_RS22930	two‑component system response regulator ArcA/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	4,630,135	0	A	G	100.0%	237.4 / NA	62	intergenic (‑12/‑84)	arcA/BW25113_RS22930	two‑component system response regulator ArcA/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (28/34);  total (28/34)

ATGCATTTCCGCGCCATCTGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCTGCATGTTTGCTACCTAAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGACCTGCCTGATGCATGCTGCAAATTAACATGATCGGCGTAACATGACTAAAGTACGTAATTGCGTTCTTGATGCACTTTCCATCAACGTCAACA  >  NZ_CP009273/4630004‑4630270                                                                                                                                    |                                                                                                                                        aTGCATTTCCGTGCCATCTGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCTGCATGTTTGCTACCTGAATTGc                                                                                                                                   >  1:1119986/1‑138 (MQ=255) aTGCATTTCCGCGCCATCTGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCTGCATGTTTGCTACCTGAATTg                                                                                                                                    <  2:824906/137‑1 (MQ=255) aTGCATTTCCGCGCCATCTGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCTGCATGTTTGCTACCTGAATTGc                                                                                                                                   >  2:34289/1‑138 (MQ=255)      tttCCGCGCCATCTGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCTGCATGTTTGCTACCTGAATTGCCAACt                                                                                                                              >  1:301955/1‑138 (MQ=255)            cgcCATCTGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCTGCATGTTTGCTACCTGAATTGCCAACTAAATCg                                                                                                                        >  1:61750/1‑138 (MQ=255)            cgcCATCTGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCTGCATGTTTGCTACCTGAATTGCCAACTAAATCg                                                                                                                        >  1:384810/1‑138 (MQ=255)                aTCTGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCTGCATGTTTGCTACCTGAATTGCCAACTAAATCGaaa                                                                                                                     >  1:595311/1‑137 (MQ=255)                aTCTGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCTGCATGTTTGCTACCTGAATTGCCAACTAAATCGAAACa                                                                                                                   <  1:1081385/139‑1 (MQ=255)                     tCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCTGCATGTTTGCTACCTGAATTGCCAACTAAATCGAAACAgg                                                                                                                 <  2:384810/136‑1 (MQ=255)                         ttCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGATGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCTGCATGTTTGCTACCTGAATTGCCAACTAAATCGAAACAGGAAGTAc                                                                                                           >  2:51440/1‑138 (MQ=255)                           cGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCTGCATGTTTGCTACCTGAATTGCCAACTAAATCGAAACAGGAAGTACaa                                                                                                         <  2:409659/138‑1 (MQ=255)                            gAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCTGCATGTTTGCTACCTGAATTGCCAACTAAATCGAAACAGGAAGTACaaa                                                                                                        <  1:633139/138‑1 (MQ=255)                            gAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCTGCATGTTTGCTACCTGAATTGCCAACTAAATCGAAACAGGAAGTACaaa                                                                                                        <  2:1119986/138‑1 (MQ=255)                            gAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCTGCATGTTTGCTACCTGAATTGCCAACTAAATCGAAACAGGAAGTACaaa                                                                                                        <  2:1157232/138‑1 (MQ=255)                                aCATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCTGCATGTTTGCTACCTGAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTcc                                                                                                   <  2:301955/139‑1 (MQ=255)                                     atAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCTGCATGTTTGCTACCTGAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGAc                                                                                              <  2:614267/139‑1 (MQ=255)                                     atAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCTGCATGTTTGCTACCTGAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGAc                                                                                              <  1:883470/139‑1 (MQ=255)                                     atAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCTGCATGTTTGCTACCTGAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGAc                                                                                              <  2:423507/139‑1 (MQ=255)                                     atAGCCTGCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCTGCATGTTTGCTACCTGAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGAc                                                                                              <  2:1140535/139‑1 (MQ=255)                                         ccTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCTGCATGTTTGCTACCTGAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGAcctgc                                                                                          <  2:691627/139‑1 (MQ=255)                                                             tttCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCTGCATGTTTGCTACCTGAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGACCTGCCTGATGCATGCTGCAAAtt                                                                       >  2:826239/1‑138 (MQ=255)                                                              ttCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCTGCATGTTTGCTACCTGAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGACCTGCCTGATGCATGCTGCAAATTaa                                                                     >  2:255200/1‑139 (MQ=255)                                                              ttCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCTGCATGTTTGCTACCTGAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGACCTGCCTGATGCATGCTGCAAATTaa                                                                     >  2:214181/1‑139 (MQ=255)                                                                   cGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCTGCATGTTTGCTACCTGAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGACCTGCCTGATGCATGCTGCAAATTAACATGa                                                                <  2:209506/139‑1 (MQ=255)                                                                   cGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCTGCATGTTTGCTACCTGAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGACCTGCCTGATGCATGCTGCAAATTAACATGa                                                                <  2:1108974/139‑1 (MQ=255)                                                                    gtgtTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCTGCATGTTTGCTACCTGAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGACCTGCCTGATGCATGCTGCAAATTAACATGAt                                                               <  1:34289/139‑1 (MQ=255)                                                                    gtgtTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCTGCATGTTTGCTACCTGAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGACCTGCCTGATGCATGCTGCAAATTAACATGAt                                                               <  1:214181/139‑1 (MQ=255)                                                                                aCCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCTGCATGTTTGCTACCTGAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGACCTGCCTGATGCATGCTGCAAATTAACATGATCGGCGTAACAt                                                    >  2:728296/1‑138 (MQ=255)                                                                                    aCTCGTCTTCAACGATAAGAATGTGCGGGGTCTGCATGTTTGCTACCTGAATTGCCAACTAAATCGAAACAgg                                                                                                                 >  2:64963/1‑73 (MQ=255)                                                                                    aCTCGTCTTCAACGATAAGAATGTGCGGGGTCTGCATGTTTGCTACCTGAATTGCCAACTAAATCGAAACAgg                                                                                                                 <  1:64963/73‑1 (MQ=255)                                                                                    aCTCGTCTTCAACGATAAGAATGTGCGGGGTCTGCATGTTTGCTACCTGAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGACCTGCCTGATGCATGCTGCAAATTAACATGATCGGCGTAACATGACt                                                >  2:1245740/1‑138 (MQ=255)                                                                                    aCTCGTCTTCAACGATAAGAATGTGCGGGGTCTGCATGTTTGCTACCTGAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGACCTGCCTGATGCATGCTGCAAATTAACATGATCGGCGTAACATGACt                                                >  2:998670/1‑138 (MQ=255)                                                                                    aCTCGTCTTCAACGATAAGAATGTGCGGGGTCTGCATGTTTGCTACCTGAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGACCTGCCTGATGCATGCTGCAAATTAACATGATCGGCGTAACATGACt                                                >  2:1123031/1‑138 (MQ=255)                                                                                         tCTTCAACGATAAGAATGTGCGGGGTCTGCATGTTTGCTACCTGAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGACCTGCCTGATGCATGCTGCAAATTAACATGATCGGCGTAAc                                                      >  2:642458/1‑127 (MQ=255)                                                                                         tCTTCAACGATAAGAATGTGCGGGGTCTGCATGTTTGCTACCTGAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGACCTGCCTGATGCATGCTGCAAATTAACATGATCGGCGTAAc                                                      <  1:642458/127‑1 (MQ=255)                                                                                               aCGATAAGAATGTGCGGGGTCTGCATGTTTGCTACCTGAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGACCTGCCTGATGCATGCTGCAAATTAACATGATCGGCGTAACATGACTAAAGTACGTAAt                                    <  1:1037896/139‑1 (MQ=255)                                                                                                  aTAAGAATGTGCGGGGTCTGCATGTTTGCTACCTGAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGACCTGCCTGATGCATGCTGCAAATTAACATGATCGGCGTAACATGACTAAAGTACGTAATTGc                                 >  1:661945/1‑139 (MQ=255)                                                                                                     aGAATGTGCGGGGTCTGCATGTTTGCTACCTGAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGACCTGCCTGATGCATGCTGCAAATTAACATGATCGGCGTAACATGACTAAAGTACGTAATTGCGt                               <  1:947275/138‑1 (MQ=255)                                                                                                     aGAATGTGCGGGGTCTGCATGTTTGCTACCTGAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGACCTGCCTGATGCATGCTGCAAATTAACATGATCGGCGTAACATGACTAAAGTACGTAATTGCGt                               <  2:411634/138‑1 (MQ=255)                                                                                                     aGAATGTGCGGGGTCTGCATGTTTGCTACCTGAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGACCTGCCTGATGCATGCTGCAAATTAACATGACCGGCGTAACATGACTAAAGTACGTAATTGCGt                               <  1:1123031/138‑1 (MQ=255)                                                                                                           tgCGGGGTCTGCATGTTTGCTACCTGAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGACCTGCCTGATGCATGCTGCAAATTAACATGATCGGCGTaa                                                       >  2:994620/1‑108 (MQ=255)                                                                                                           tgCGGGGTCTGCATGTTTGCTACCTGAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGACCTGCCTGATGCATGCTGCAAATTAACATGATCGGCGTaa                                                       <  1:994620/108‑1 (MQ=255)                                                                                                            gCGGGGTCTGCATGTTTGCTACCTGAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGa                                                                                               >  1:521295/1‑67 (MQ=255)                                                                                                            gCGGGGTCTGCATGTTTGCTACCTGAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGa                                                                                               <  2:521295/67‑1 (MQ=255)                                                                                                                ggTCTGCATGTTTGCTACCTGAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGACCTGCCTGATGCATGCTGCAAATTAACATGGTCGGCGTAACATGACTAAAGTACGTAATTGCGTTCTTGATGCGCt                   <  2:175299/139‑1 (MQ=255)                                                                                                                 gTCTGCATGTTTGCTACCTGAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGAc                                                                                              <  1:597237/63‑1 (MQ=255)                                                                                                                 gTCTGCATGTTTGCTACCTGAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGAc                                                                                              >  2:597237/1‑63 (MQ=255)                                                                                                                    tGCATGTTTGCTACCTGAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGACCTGCCTGATGCATGCTGCAAATTAACATGATCGGCGTAACATGACTAAAGTACGTAATTGCGTTCTTGATGCACTTTc                >  1:775439/1‑138 (MQ=255)                                                                                                                     gCATGTTTGCTACCTGAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGGCCTGCCTGATGCATGCTGCAAATTAACATGATCGGCGTAACATGACTAAAGTACGTAATTGCGTTCTTGATGCACTTTCCa              >  1:1034053/1‑139 (MQ=255)                                                                                                                     gCATGTTTGCTACCTGAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGACCTGCCTGATGCATGCTGCaa                                                                          >  1:1174757/1‑79 (MQ=255)                                                                                                                     gCATGTTTGCTACCTGAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGACCTGCCTGATGCATGCTGCaa                                                                          <  2:1174757/79‑1 (MQ=255)                                                                                                                          tttGCTACCTGAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGACCTGCCTGATGCATGCTGCAAATTAACATGATCGGCGTAACATGACTAAAGTACGTAATTGCGTTCTTGATGCACTTTCCATCAAc         <  2:428863/139‑1 (MQ=255)                                                                                                                            tGCTACCTGAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGACCTGCCTGATGCATGCTGCAAATTAACATGAt                                                               <  1:360588/83‑1 (MQ=255)                                                                                                                            tGCTACCTGAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGACCTGCCTGATGCATGCTGCAAATTAACATGAt                                                               >  2:360588/1‑83 (MQ=255)                                                                                                                            tGCTACCTGAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGACCTGCCTGATGCATGCTGCAAATTAACATGATCGGCGTAACATGACTAAAGTACGTAATTGCGTTCTTGATGCACTTTCCATCAACGt       >  1:309361/1‑139 (MQ=255)                                                                                                                            tGCTACCTGAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGACCTGCCTGATGCATGCTGCAAATTAACATGATCGGCGTAACATGACTAAAGTACGTAATTGCGTTCTTGATGCACTTTCCATCAACGt       >  1:260204/1‑139 (MQ=255)                                                                                                                                aCCTGAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGACCTGCCTGATGCATGCTGCAAATTAACATGATCGGCGTAACATGACTAAAGTACGTAATTGCGt                               >  2:1092734/1‑111 (MQ=255)                                                                                                                                aCCTGAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGACCTGCCTGATGCATGCTGCAAATTAACATGATCGGCGTAACATGACTAAAGTACGTAATTGCGt                               <  1:1092734/111‑1 (MQ=255)                                                                                                                                aCCTGAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGACCTGCCTGATGCATGCTGCAAATTAACATGATCGGCGTAACATGACTAAAGTACGTAATTGCGTTCTTGATGCACTTTCCATCAACGTcaa    >  2:1046389/1‑138 (MQ=255)                                                                                                                                 ccTGAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGACCTGCCTGATGCATGCTGCAAATTAACATGATCGGCGTAACATGACTAAAGTACGTAATTGCGTTCTTGATGCACTTTCCATCAACGTcaaca  <  2:61750/139‑1 (MQ=255)                                                                                                                                 ccTGAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGACCTGCCTGATGCATGCTGCAAATTAACATGATCGGCGTAACATGACTAAAGTACGTAATTGCGTTCTTGATGCACTTTCCATCAACGTcaaca  <  1:1245740/139‑1 (MQ=255)                                                                                                                                 ccTGAATTGCCAACTAAAACGAAACAGGAAGTACAAAAGTCCCTGACCTGCCTGATGCATGCTGCAAATTAACATGATCGGCGTAACATGACTAAAGTACGTAATTGCGTTCTTGATGCACTTTCCATCAACGTcaaca  <  2:1145349/139‑1 (MQ=255)                                                                                                                                    |                                                                                                                                        ATGCATTTCCGCGCCATCTGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCTGCATGTTTGCTACCTAAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGACCTGCCTGATGCATGCTGCAAATTAACATGATCGGCGTAACATGACTAAAGTACGTAATTGCGTTCTTGATGCACTTTCCATCAACGTCAACA  >  NZ_CP009273/4630004‑4630270

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: ‑