Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,104,659	C→A	R106L (CGT→CTT)	cpxA ←	sensory histidine kinase CpxA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,104,659	0	C	A	100.0%	194.9 / NA	56	R106L (CGT→CTT)	cpxA	sensory histidine kinase CpxA
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (22/34);  total (22/34)

AACTGCTGGCCGGACGAATCAGATAAAGTTGGTAATTATCTTCGCCATCACGCACGGAGAACGGACCGACCAGTTCCACGCGGCCATACTTTTTCTTCTGCGGATGATCGGCGTTATCGGCCTGACCAATAAAGTTACGAATGATCTGCATTTCGCTGCGTTCAGCGCCGATCACGCGGCCTTC‑GGTGGTCACCAATAACAAACGCTGTCCTGGCGGTGCCCACTTATCAATCGCCCGGAACAGACGCCGCCACCACATTAAATCGTTGGGCG  >  NC_000913/4104522‑4104794                                                                                                                                          |                                                                                                                                         aaCTGCTGGCCGGACGAATCAGATAAAGTTGGTAATTATCTTCGCCATCACGCACGGAGAACGGACCGACCAGTTCCACGCGGCCATACTTTTTCTTCTGCGGATGATCGGCGTTATCGGCCTGACCAATAAAGTTAAGa                                                                                                                                        <  2:368118/140‑1 (MQ=255) aaCTACTGGCCGGACGAATCAGATAAAGTTGGTAATTATCTTCGCCATCACGCACGGAGAACGGACCGACCAGTTCCACGCGGCCATACTTTTTCTTCTGCGGATGATCGGCGTTATCGGCCTGACCAATAAAGTTAAGa                                                                                                                                        <  1:911851/140‑1 (MQ=255)    tgctgGCCGGACGAATCAGATAAAGTTGGTAATTATCTTCGCCATCACGCACGGAGAACGGACCGACCAGTTCCACGCGGCCATACTTTTTCTTCTGCGGATGATCGGCGTTATCGGCCTGACCAATAAAGTTAAGAATg                                                                                                                                     >  1:930039/1‑140 (MQ=255)     gctgGCCGGACGAATCAGATAAAGTTGGTAATTATCTTCGCCATCACGCACGGAGAACGGACCGACCAGTTCCACGCGGCCATACTTTTTCTTCTGCGGATGATCGGCGTTATCGGCCTGACCAATAAAGTTAAGAATGa                                                                                                                                    >  2:122221/1‑140 (MQ=255)     gctgGCCGGACGAATCAGATAAAGTTGGTAATTATCTTCGCCATCACGCACGGAGAACGGACCGACCAGTTCCACGCGGCCATACTTTTTCTTCTGCGGATGATCGGCGTTATCGGCCTGACCAATAAAGTTAAGAATGa                                                                                                                                    >  1:406615/1‑140 (MQ=255)         gCCGGACGAATCAGATAAAGTTGGTAATTATCTTCGCCATCACGCACGGAGAACGGACCGACCAGTTCCACGCGGCCATACTTTTTCTTCTGCGGATGATCGGCGTTATCGGCCTGACCAATAAAGTTAAGAATGATCTg                                                                                                                                >  2:300648/1‑140 (MQ=255)           cGGACGAATCAGATAAAGTTGGTAATTATCTTCGCCATCACGCACGGAGAACGGACCGACCAGTTCCACGCGGCCATACTTTTTCTTCTGCGGATGATCGGCGTTATCGGCCTGACCAATAAAGTTAAGAATGATCTGCa                                                                                                                              >  1:1241552/1‑140 (MQ=255)                  aTCAGATAAAGTTGGTAATTATCTTCGCCATCACGCACGGAGAACGGACCGACCAGTTCCACGCGGCCATACTTTTTCTTCTGCGGATGATCGGCGTTATCGGCCTGACCAATAAAGTTAAGAATGATCTGCATTTCGCt                                                                                                                       <  1:615287/140‑1 (MQ=255)                  aTCAGATAAAGTTGGTAATTATCTTCGCCATCACGCACGGAGAACGGACCGACCAGTTCCACGCGGCCATACTTTTTCTTCTGCGGATGATCGGCGTTATCGGCCTGACCAATAAAGTTAAGAATGATCTGCATTTCGCt                                                                                                                       <  1:980863/140‑1 (MQ=255)                               ggTAATTATCTTCGCCATCACGCACGGAGAACGGACCGACCAGTTCCACGCGGCCATACTTTTTCTTCTGCGGATGATCGGCGTTATCGGCCTGACCAATAAAGTTAAGAATGATCTGCATTTCGCTGCGTTCAGCGCCg                                                                                                          <  2:930039/140‑1 (MQ=255)                                 tAATTATCTTCGCCATCACGCACGGAGAACGGACCGACCAGTTCCACGCGGCCATACTTTTTCTTCTGCGGATGATCGGCGTTATCGGCCTGACCAATAAAGTTAAGAATGATCTGCATTTCGCTGCGTTCAGGGCCGAt                                                                                                        >  1:817157/1‑140 (MQ=255)                                 tAATTATCTTCGCCATCACGCACGGAGAACGGACCGACCAGTTCCACGCGGCCATACTTTTTCTTCTGCGGATGATCGGCGTTATCGGCCTGACCAATAAAGTTAAGAATGATCTGCATTTCGCTGCGTTCAGCGCCGAt                                                                                                        >  2:1122543/1‑140 (MQ=255)                                     tATCTTCGCCATCACGCACGGAGAACGGACCGACCAGTTCCACGCGGCCATACTTTTTCTTCTGCGGATGATCGGCGTTATCGGCCTGACCAATAAAGTTAAGAATGATCTGCATTTCGCTGCGTTCAGCGCCGATCAcg                                                                                                    <  2:894215/140‑1 (MQ=255)                                      aTCTTCGCCATCACGCACGGAGAACGGACCGACCAGTTCCACGCGGCCATACTTTTTCTTCTGCGGATGATCGGCGTTATCGGCCTGACCAATAAAGTTAAGAATGATCTGCATTTCGCTGCGTTCAGCGCCGATCAcgc                                                                                                   <  2:1145614/140‑1 (MQ=255)                                          tCGCCATCACGCACGGAGAACGGACCGACCAGTTCCACGCGGCCATACTTTTTCTTCTGCGGATGATCGGCGTTATCGGCCTGACCAATAAAGTTAAGAATGATCTGCATTTCGCTGCGTTCAGCGCCGATCACGCGGcc                                                                                               >  2:300587/1‑140 (MQ=255)                                            gCCATCACGCACGGAGAACGGACCGACCAGTTCCACGCGGCCATACTTTTTCTTCTGCGGATGATCGGCGTTATCGGCCTGACCAATAAAGTTAAGAATGATCTGCATTTCGCTGCGTTCAGCGCCGATCACGCGGCCtt                                                                                             <  2:734173/140‑1 (MQ=255)                                              cATCACGCACGGAGAACGGACCGACCAGTTCCACGCGGCCATACTTTTTCTTCTGCGGATGATCGGCGTTATCGGCCTGACCAATAAAGTTAAGAATGATCTGCATTTCGCTGCGTTCAGCGCCGATCACGCGGCCTTC‑g                                                                                          >  2:676438/1‑140 (MQ=255)                                                 cacgcacgGAGAACGGACCGACCAGTTCCACGCGGCCATACTTTTTCTTCTGCGGATGATCGGCGTTATCGGCCTGACCAATAAAGTTAAGAATGATCTGCATTTCGCTGCGTTCAGCGCCGATCACGCGGCCTTC‑ggtg                                                                                       <  1:1122543/140‑1 (MQ=255)                                                 cacgcacgGAGAACGGACCGACCAGTTCCACGCGGCCATACTTTTTCTTCTGCGGATGATCGGCGTTATCGGCCTGACCAATAAAGTTAAGAATGATCTGCATTTCGCTGCGTTCAGCGCCGATCACGCGGCCTTC‑ggtg                                                                                       >  2:982748/1‑140 (MQ=255)                                                        ggAGAACGGACCGACCAGTTCCACGCGGCCATACTTTTTCTTCTGCGGATGATCGGCGTTATCGGCCTGACCAATAAAGTTAAGAATGATCTGCATTTCGCTGCGTTCAGCGCCGATCACGCGGCCTTC‑GGTGGTCACCa                                                                                >  2:493330/1‑140 (MQ=255)                                                        ggAGAACGGACCGACCAGTTCCACGCGGCCATACTTTTTCTTCTGCGGATGATCGGCGTTATCGGCCTGACCAATAAAGTTAAGAATGATCTGCATTTCGCTGCGTTCAGCGCCGATCACGCGGCCTTC‑GGTGGTCACCa                                                                                <  1:401917/140‑1 (MQ=255)                                                              cGGACCGACCAGTTCCACGCGGCCATACTTTTTCTTCTGCGGATGATCGGCGTTATCGGCCTGACCAATAAAGTTAAGAATGATCTGCATTTCGCTGCGTTCAGCGCCGATCACGCGGCCTTC‑GGTGGTCACCAATAACa                                                                          >  1:198948/1‑140 (MQ=255)                                                                gaccgaccAGTTCCACGCGGCCATACTTTTTCTTCTGCGGATGATCGGCGTTATCGGCCTGACCAATAAAGTTAAGAATGATCTGCATTTCGCTGCGTTCAGCGCCGATCACGCGGCCTTC‑GGTGGTCACCAATAACaaa                                                                        <  1:122221/140‑1 (MQ=255)                                                                  ccgaccAGTTCCACGCGGCCATACTTTTTCTTCTGCGGATGATCGGCGTTATCGGCCTGACCAATAAAGTTAAGAATGATCTGCATTTCGCTGCGTTCAGGGCCGATCACGCGGCCTTC‑GGTGGTCACCAATAACAAACg                                                                      <  2:817157/140‑1 (MQ=255)                                                                  ccgaccAGTTCCACGCGGCCATACTTTTTCTTCTGCGGATGATCGGCGTTATCGGCCTGACCAATAAAGTTAAGAATGATCTGCATTTCGCTGCGTTCAGCGCCGATCACGCGGCCTTC‑GGTGGTCACCAATAACAAACg                                                                      <  2:830537/140‑1 (MQ=255)                                                                           tCCACGCGGCCATACTTTTTCTTCTGCGGATGATCGGCGTTATCGGCCTGACCAATAAAGTTAAGAATGATCTGCATTTCGCTGCGTTCAGCGCCGATCACGCGGCCTTC‑GGTGGTCACCAATAACAAACGCTGTCCTgg                                                             <  1:676438/140‑1 (MQ=255)                                                                           tCCACGCGGCCATACTTTTTCTTCTGCGGATGATCGGCGTTATCGGCCTGACCAATAAAGTTAAGAATGATCTGCATTTCGCTGCGTTCAGCGCCGATCACGCGGCCTTC‑GGTGGTCACCAATAACAAACGCTGTCCTgg                                                             <  1:300648/140‑1 (MQ=255)                                                                             cACGCGGCCATACTTTTTCTTCTGCGGATGATCGGCGTTATCGGCCTGACCAATAAAGTTAAGAATGATCTGCATTTCGCTGCGTTCAGCGCCGATCACGCGGCCTTC‑GGTGGTCACCAATAACAAACGCTGTCCTGGCg                                                           >  1:333208/1‑140 (MQ=255)                                                                               cgcgGCCATACTTTTTCTTCTGCGGATGATCGGCGTTATCGGCCTGACCAATAAAGTTAAGAATGATCTGCATTTCGCTGCATTCAGCGCCGATCACGCGGCCTTC‑GGTGGTCACCAATAACAAACGCTGTCCTGGCGGt                                                         >  2:1220874/1‑140 (MQ=255)                                                                               cgcgGCCATACTTTTTCTTCTGCGGATGATCCGCGTTATCGGCCTGACCAATAAAGTTAAGAATGATCTGCATTTCGCTGCGTTCAGCGCCGATCACGCGGCCTTC‑GGTGGTCACCAATAACAAACGCTGTCCTGGCggg                                                         >  2:726984/1‑139 (MQ=255)                                                                                gcgGCCATACTTTTTCTTCTGCGGATGATCGGCGTTATCGGCCTGACCAATAAAGTTAAGAATGATCTGCATTTCGCTGCGTTCAGCGCCGATCACGCGGCCTTC‑GGTGGTCACCAATAACAAACGCTGTCCTGGCGGTg                                                        <  2:81916/140‑1 (MQ=255)                                                                                  ggCCATACTTTTTCTTCTGCGGATGATCGGCGTTATCGGCCTGACCAATAAAGTTAAGAATGATCTGCATTTCGCTGCGTTCAGCGCCGATCACGCGGCCTTC‑GGTGGTCACCAATAACAAACGCTGTCCTGGCGGTGcc                                                      <  1:416219/140‑1 (MQ=255)                                                                                  ggCCATACTTTTTCTTCTGCGGATGATCGGCGTTATCGGCCTGACCAATAAAGTTAAGAATGATCTGCATTTCGCTGCGTTCAGCGCCGATCACGCGGCCTTC‑GGTGGTCACCAATAACAAACGCTGTCCTGGCGGTGcc                                                      <  1:964124/140‑1 (MQ=255)                                                                                  ggCCATACTTTTTCTTCTGCGGATGATCGGCGTTATCGGCCTGACCAATAAAGTTAAGAATGATCTGCATTTCGCTGCGTTCAGCGCCGATCACGCGGCCTTC‑GGTGGTCACCAATAACAAACGCTGTCCTGGCGGTGcc                                                      <  1:542644/140‑1 (MQ=255)                                                                                  ggCCATACTTTTTCTTCTGCGGATGATCGGCGTTATCGGCCTGACCAATAAAGTTAAGAATGATCTGCATTTCGCTGCGTTCAGCGCCGATCACGCGGCCTTC‑GGTGGTCACCAATAACAAACGCTGTCCTGGCGGTGcc                                                      <  2:1241552/140‑1 (MQ=255)                                                                                  ggCCATACTTTTTCTTCTGCGGATGATCGGCGTTATCGGCCTGACCAATAAAGTTAAGAATGATCTGCATTTCGCTGCGTTCAGCGCCGATCACGCGGCCTTC‑GGTGGTCACCAATAACAAACGCTGTCCTGGCGGTGcc                                                      <  2:409025/140‑1 (MQ=255)                                                                                    ccATACTTTTTCTTCTGCGGATGATCGGCGTTATCGGCCTGACCAATAAAGTTAAGAATGATCTGCATTTCGCTGCGTTCAGCGCCGATCACGCGGCCTTC‑GGTGGTCACCAATAACAAACGCTGTCCTGGCGGTGCCCa                                                    >  1:1180927/1‑140 (MQ=255)                                                                                       tACTTTTTCTTCTGCGGATGATCGGCGTTATCGGCCTGACCAATAAAGTTAAGAATGATCTGCATTTCGCTGCGTTCAGCGCCGATCACGCGGCCTTC‑GGTGGTCACCAATAACAAACGCTGTCCTGGCGGTGCCCACtt                                                 <  1:300587/140‑1 (MQ=255)                                                                                              tcttctGCGGATGATCGGCGTTATCGGCCTGACCAATAAAGTTAAGAATGATCTGCATTTCGCTGCGTTCAGCGCCGATCACGCGGCCTTC‑GGTGGTCACCAATAACAAACGCTGTCCTGGCGGTGCCCACTTATCAATc                                          <  1:493330/140‑1 (MQ=255)                                                                                                 tctGCGGATGATCGGCGTTATCGGCCTGACCAATAAAGTTAAGAATGATCTGCATTTCGCTGCGTTCAGCGCCGATCACGCGGCCTTC‑GGTGGTCACCAATAACAAACGCTGTCCTGGCGGTGCCCACTTATCAATCGcc                                       <  2:1187344/140‑1 (MQ=255)                                                                                                  ctGCGGATGATCGGCGTTATCGGCCTGACCAATAAAGTTAAGAATGATCTGCATTTCGCTGCGTTCAGCGCCGATCACGCGGCCTTC‑GGTGGTCACCAATAACAAACGCTGTCCTGGCGGTGCCCACTTATCAATCGccc                                      >  1:787825/1‑140 (MQ=255)                                                                                                   tGCGGATGATCGGCGTTATCGGCCTGACCAATAAAGTTAAGAATGATCTGCATTTCGCTGCGTTCAGCGCCGATCACGCGGCCTTCGGGTGGTCACCAATAACAAACGCTGTCCTGGCGGTGCCCACTTATCAATCGccc                                      >  2:585286/1‑140 (MQ=255)                                                                                                    gCGGATGATCGGCGTTATCGGCCTGACCAATAAAGTTAAGAATGATCTGCATTTCGCTGCGTTCAGCGCCGATCACGCGGCCTTC‑GGTGGTCACCAATAACAAACGCTGTCCTGGCGGTGCCCACTTATCAATCGCCCgg                                    >  1:626117/1‑140 (MQ=255)                                                                                                               gCGTTATCGGCCTGACCAATAAAGTTAAGAATGATCTGCATTTCGCTGCGTTCAGCGCCGATCACGCGGCCTTC‑GGTGGTCACCAATAACAAACGCTGTCCTGGCGGTGCCCACTTATCAATCGCCCGGAACAGAcgccg                         <  2:1127619/140‑1 (MQ=255)                                                                                                                   tATCGGCCTGACCAATAAAGTTAAGAATGATCTGCATTTCGCTGCGTTCAGCGCCGATCACGCGGCCTTC‑GGTGGTCACCAATAACAAACGCTGTCCTGGCGGTGCCCACTTATCAATCGCCCGGAACAGACGCCGccac                     <  2:1092031/140‑1 (MQ=255)                                                                                                                   tATCGGCCTGACCAATAAAGTTAAGAATGATCTGCATTTCGCTGCGTTCAGCGCCGATCACGCGGCCTTC‑GGTGGTCACCAATAACAAACGCTGTCCTGGCGGTGCCCACTTATCAATCGCCCGGAACAGACGCCGccac                     <  2:384990/140‑1 (MQ=255)                                                                                                                   tATCGGCCTGACCAATAAAGTTAAGAATGATCTGCATTTCGCTGCGTTCAGCGCCGATCACGCGGCCTTC‑GGTGGTCACCAATAACAAACGCTGTCCTGGCGGTGCCCACTTATCAATCGCCCGGAACAGACGCCGccac                     <  2:1238102/140‑1 (MQ=255)                                                                                                                       ggCCTGACCAATAAAGTTAAGAATGATCTGCATTTCGTTGCGTTCAGCGCCGATCACGCGGCCTTC‑GGTGGTCACCAATAACAAACGCTGTCCTGGCGGTGCCCACTTATCAATCGCCCGGAACAGACGCCGCCACcaca                 <  2:57546/140‑1 (MQ=255)                                                                                                                          cTGACCAATAAAGTTAAGAATGATCTGCATTTCGCTGCGTTCAGCGCCGATCACGCGGCCTTCGGGTGGTCACCAATAACAAACGCTGTCCTGGCGGTGCCCACTTATCAATCGCCCGGAACAGACGCCGCCACCACAtt               <  1:585286/140‑1 (MQ=255)                                                                                                                          cTGACCAATAAAGTTAAGAATGATCTGCATTTCGCTGCGTTCAGCGCCGATCACGCGGCCTTC‑GGTGGTCACCAATAACAAACGCTGTCCTGGCGGTGCCCACTTATCAATCGCCCGGAACAGACGCCGCCACCACATTa              >  2:1006743/1‑140 (MQ=255)                                                                                                                          cTGACCAATAAAGTTAAGAATGATCTGCATTTCGCTGCGTTCAGCGCCGATCACGCGGCCTTC‑GGTGGTCACCAATAACAAACGCTGTCCTGGCGGTGCCCACTTATCAATCGCCCGGAACAGACGCCGCCACCACATTa              >  1:344263/1‑140 (MQ=255)                                                                                                                            gACCAATAAAGTTAAGAATGATCTGCATTTCGCTGCGTTCAGCGCCGATCACGCGGCCTTC‑GGTGGTCACCAATAACAAACGCTGTCCTGGCGGTGCCCACTTATCAATCGCCCGGAACAGACGCCGCCACCACATTaaa            >  2:121854/1‑140 (MQ=255)                                                                                                                            gACCAATAAAGTTAAGAATGATCTGCATTTCGCTGCGTTCAGCGCCGATCACGCGGCCTTC‑GGTGGTCACCAATAACAAACGCTGTCCTGGCGGTGCCCACTTATCAATCGCCCGGAACAGACGCCGCCACCACATTaaa            <  2:787825/140‑1 (MQ=255)                                                                                                                               cAATAAAGTTAAGAATGATCTGCATTTCGCTGCGTTCAGCGCCGATCACGCGGCCTTC‑GGTGGTCACCAATAACAAACGCTGTCCTGGCGGTGCCCACTTATCAATCGCCCGGAACAGACGCCGCCACCACATTAAATCg         <  2:1206282/140‑1 (MQ=255)                                                                                                                                  tAAAGTTAAGAATGATCTGCATTTCGCTGCGTTCAGCGCCGATCACGCGGCCTTC‑GGTGGTCACCAATAACAAACGCTGTCCTGGCGGTGCCCACTTATCAATCGCCCGGAACAGACGCCGCCACCACATTAAATCGTTg      >  1:313624/1‑140 (MQ=255)                                                                                                                                      gTTAAGAATGATCTGCATTTCGCTGCGTTCAGCGCCGATCACGCGGCCTTC‑GGTGGTCACCAATAACAAACGCTGTCCTGGCGGTGCCCACTTATCAATCGCCCGGAACAGACGCCGCCACCACATTAAATCGTTGGGCg  <  1:721072/140‑1 (MQ=255)                                                                                                                                       ttAAGAATGATCTGCATTTCGCTGCGTTCAGCGCCGATCACGCGGCCTTC‑GGTGGTCACCAATAACAAACGCTGTCCTGGCGGTGCCCACTTATCAATCGCCCGGAACAGACGCCGCCACcaca                 <  1:113115/124‑1 (MQ=255)                                                                                                                                          |                                                                                                                                         AACTGCTGGCCGGACGAATCAGATAAAGTTGGTAATTATCTTCGCCATCACGCACGGAGAACGGACCGACCAGTTCCACGCGGCCATACTTTTTCTTCTGCGGATGATCGGCGTTATCGGCCTGACCAATAAAGTTACGAATGATCTGCATTTCGCTGCGTTCAGCGCCGATCACGCGGCCTTC‑GGTGGTCACCAATAACAAACGCTGTCCTGGCGGTGCCCACTTATCAATCGCCCGGAACAGACGCCGCCACCACATTAAATCGTTGGGCG  >  NC_000913/4104522‑4104794

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑