Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,105,396	A→T	L92Q (CTG→CAG)	cpxR ←	response regulator in two‑component regulatory system with CpxA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,105,396	0	A	T	97.4%	267.5 / ‑1.6	76	L92Q (CTG→CAG)	cpxR	response regulator in two‑component regulatory system with CpxA
Reads supporting (aligned to +/- strand):  ref base A (2/0);  new base T (36/38);  total (38/38)
Fisher's exact test for biased strand distribution p-value = 4.93e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.89e-01

CTGTTGCTCGCTCCAGTGCGAACGGCGCAGGATCGCGCGAATACGTGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCAGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACAGGCGTCTGGTGTGTCTGGCGAAGTGCTTTTAATGTGTCGA  >  NC_000913/4105299‑4105492                                                                                                  |                                                                                                 cTGTTGCTCGCTCCAGTGCGAACGGCGCAGGATCGCGCGAATACGTGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGc                                                                                                <  2:281526/100‑1 (MQ=255)     tGCTCGCTCCAGTGCGAACGGCGCAGGATCGCGCGAATACGTGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCaa                                                                                            >  1:849923/1‑100 (MQ=255)      gctcgctcCAGTGCGAACGGCGCAGGATCGCGCGAATACGTGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAg                                                                                           <  1:934489/100‑1 (MQ=255)       ctcgctcCAGTGCGAACGGCGCAGGATCGCGCGAATACGTGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAgg                                                                                          <  1:503239/100‑1 (MQ=255)        tcgctcCAGTGCGAACGGCGCAGGATCGCGCGAATACGTGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGc                                                                                         >  1:1334071/1‑100 (MQ=255)         cgctcCAGTGCGAACGGCGCAGGATCGCGCGAATACGTGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGcc                                                                                        <  2:1697749/100‑1 (MQ=255)         cgctcCAGTGCGAACGGCGCAGGATCGCGCGAATACGTGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGcc                                                                                        <  2:1960504/100‑1 (MQ=255)           ctcCAGTGCGAACGGCGCAGGATCGCGCGAATACGTGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCga                                                                                      <  2:637955/100‑1 (MQ=255)           ctcCAGTGCGAACGGCGCAGGATCGCGCGAATACGTGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCga                                                                                      <  1:46460/100‑1 (MQ=255)            tcCAGTGCGAACGGCGCAGGATCGCGCGAATACGTGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCgag                                                                                     <  2:1095880/100‑1 (MQ=255)             ccAGTGCGAACGGCGCAGGATCGCGCGAATACGTGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCgaga                                                                                    >  1:1296510/1‑100 (MQ=255)                gTGCGAACGGCGCAGGATCGCGCGAATACGTGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAAcg                                                                                 >  2:594630/1‑100 (MQ=255)                 tGCGAACGGCGCAGGATCGCGCGAATACGTGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAAcgc                                                                                <  1:1805572/100‑1 (MQ=255)                 tGCGAACGGCGCAGGATCGCGCGAATACGTGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAAcgc                                                                                <  2:221104/100‑1 (MQ=255)                  gCGAACGGCGCAGGATCGCGCGAATACGTGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAAcgcg                                                                               >  2:2231634/1‑100 (MQ=255)                  gCGAACGGCGCAGGATCGCGCGAATACGTGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAAcgcg                                                                               >  2:2200232/1‑100 (MQ=255)                   cGAACGGCGCAGGATCGCGCGAATACGTGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGa                                                                              >  1:1391493/1‑100 (MQ=255)                      tctgcgcAGGATCGCGCGAATACGTGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCa                                                                           <  1:70381/97‑1 (MQ=255)                        ggCGCAGGATCGCGCGAATACGTGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAg                                                                         <  1:594631/100‑1 (MQ=255)                         gcgcAGGATCGCGCGAATACGTGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAga                                                                        >  2:70379/1‑99 (MQ=255)                         gcgcAGGATCGCGCGAATACGTGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGt                                                                        <  2:1334068/100‑1 (MQ=255)                           gcAGGATCGCGCGAATACGTGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTc                                                                      <  1:307466/100‑1 (MQ=255)                            cAGGATCGCGCGAATACGTGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCa                                                                     <  1:1403090/100‑1 (MQ=255)                            cAGGATCGCGCGAATACGTGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCa                                                                     <  1:2152091/100‑1 (MQ=255)                              ggATCGCGCGAATACGTGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACt                                                                   >  2:1835441/1‑100 (MQ=255)                              ggATCGCGCGAATACGTGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACt                                                                   >  1:1343888/1‑100 (MQ=255)                                aTCGCGCGAATACGTGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGc                                                                 <  1:2200240/100‑1 (MQ=255)                                   gcgcgAATACGTGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCcgc                                                              >  1:2070509/1‑100 (MQ=255)                                      cgAATACGTGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCcgcgcg                                                           >  1:646531/1‑100 (MQ=255)                                        aaTACGTGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGcc                                                         >  2:1884384/1‑100 (MQ=255)                                          tACGTGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCg                                                        <  2:1297053/99‑1 (MQ=255)                                            cGTGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCa                                                     >  2:1965502/1‑100 (MQ=255)                                            cGTGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCa                                                     >  2:747307/1‑100 (MQ=255)                                            cGTGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCa                                                     >  1:2159169/1‑100 (MQ=255)                                              tGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAAc                                                   >  2:365818/1‑100 (MQ=255)                                                ccaccaGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACAt                                                 <  2:345860/100‑1 (MQ=255)                                                ccaccaGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACAt                                                 <  2:1097780/100‑1 (MQ=255)                                                 caccaGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATa                                                >  1:1643242/1‑100 (MQ=255)                                                 caccaGCTCACGATCATTAAACGGTTTCGGGAGATAGTCAACTGCGCCCTGATCAAGGCCGAGAACGCCATCAAGTACACTGCCGCGCGCCGTCAACAt                                                 <  2:999386/99‑1 (MQ=255)                                                  accaGCTCACGATCATTAAACGGTTTCGGGAGATAGTCGTCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATaa                                               >  1:598776/1‑100 (MQ=255)                                                       cTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACa                                          >  2:844813/1‑100 (MQ=255)                                                       cTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACa                                          >  1:1883838/1‑100 (MQ=255)                                                        tCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACAg                                         <  2:573905/100‑1 (MQ=255)                                                         cACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACAgg                                        <  1:773689/100‑1 (MQ=255)                                                         cACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACAgg                                        >  1:1555200/1‑100 (MQ=255)                                                           cGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACAGGCg                                      >  2:1734483/1‑100 (MQ=255)                                                               cATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACAGGCGTCTg                                  >  2:2272426/1‑100 (MQ=255)                                                               cATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACAGGCGTCTg                                  >  1:883150/1‑100 (MQ=255)                                                                aTTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACAGGCGTCTgg                                 >  2:305116/1‑100 (MQ=255)                                                                  tAAACGGTTTCGGGAGATAGTCGTCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACAGGCGTCTGgtg                               <  2:598775/100‑1 (MQ=255)                                                                  tAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACAGGCGTCTGgtg                               <  1:174770/100‑1 (MQ=255)                                                                    aaCGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACAGGCGTCTGgtgtg                             >  2:699282/1‑100 (MQ=255)                                                                    aaCGGTTTCGGGAGATAGTCATCTGCGCCCAGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACAGGCGTCTGgtgtg                             >  1:2192256/1‑100 (MQ=255)                                                                      cGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACAGGCGTCTGGTGTGTc                           <  1:2320817/100‑1 (MQ=255)                                                                        gTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACAGGCGTCTGGTGTGTCTg                         >  2:193193/1‑100 (MQ=255)                                                                         tttCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACAGGCGTCTGGTGTGTCTgg                        <  1:773066/100‑1 (MQ=255)                                                                          ctCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACAGGCGTCTGGTGTGTCTGGc                       <  1:1345878/99‑1 (MQ=255)                                                                            cGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACAGGCGTCTGGTGTGTCTGGcag                     >  2:1345875/1‑98 (MQ=255)                                                                              ggAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACAGGCGTCTGGTGTGTCTGGCGAAg                   <  1:453865/100‑1 (MQ=255)                                                                              ggAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACAGGCGTCTGGTGTGTCTGGCGAAg                   <  2:962570/100‑1 (MQ=255)                                                                               gagaTAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACAGGCGTCTGGTGTGTCTGGCGAAGt                  <  2:1296507/100‑1 (MQ=255)                                                                               gagaTAGTCATATGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCACCATAATGACAGGCGTCTGGTGTGTCTGGCGAAGt                  >  2:1233320/1‑100 (MQ=255)                                                                                   tAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACAGGCGTCTGGTGTGTCTGGCGAAGTGCtt              <  2:1555196/100‑1 (MQ=255)                                                                                   tAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACAGGCGTCTGGTGTGTCTGGCGAAGTGCtt              >  2:1845718/1‑100 (MQ=255)                                                                                    aGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACAGGCGTCTGGTGTGTCTGGCGAAGTGCttt             <  1:2231642/100‑1 (MQ=255)                                                                                     gTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACAGGCGTCTGGTGTGTCTGGCGAAGTGCtttt            <  1:1856400/100‑1 (MQ=255)                                                                                       cATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACAGGCGTCTGGTGTGTCTGGCGAAGTGCTTTTaa          >  2:1714602/1‑100 (MQ=255)                                                                                       cATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACAGGCGTCTGGTGTGTCTGGAGAAGTGCTTTTaa          >  1:1599166/1‑100 (MQ=255)                                                                                        aTCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACAGGCGTCTGGTGTGTCTGGCGAAGTGCTTTTAAt         <  2:1589449/100‑1 (MQ=255)                                                                                         tCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACAGGCGTCTGGTGTGTCTGGCGAAGTGCTTTTAAtg        <  1:1884391/100‑1 (MQ=255)                                                                                         tCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACAGGCGTCTGGTGTGTCTGGCGAAGTGCTTTTAAtg        <  1:274346/100‑1 (MQ=255)                                                                                             cgcCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACAGGCGTCTGGTGTGTCTGGCGAAGTGCTTTTAATGTGTc    >  1:246291/1‑100 (MQ=255)                                                                                             cgcCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGAGCGCCGTCAACATAATGACCGGCGTCTGGTGTGTCTGGCGAAGTGCTTTTAATGTGTc    >  2:1275519/1‑100 (MQ=255)                                                                                             cgcCCTGCTCAAGGCCGAGAACGCGATCAAGTACACTGCCGCGCGCCGTCAACATAATGACAGGCGTCTGGTGTGTCTGGCGAAGTGCTTTTAATGTGTc    <  2:1642127/100‑1 (MQ=255)                                                                                               cccTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACAGGCGTCTGGTGTGTCTGGCGAAGTGCTTTTAATGTGTCGa  >  1:29930/1‑100 (MQ=255)                                                                                               cccAGCTCTAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACAGGCGTCTGGTGTGCCTGGCGAAGTGCTTTTAATGTGTCGa  >  2:727478/1‑100 (MQ=255)                                                                                                  |                                                                                                 CTGTTGCTCGCTCCAGTGCGAACGGCGCAGGATCGCGCGAATACGTGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCAGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACAGGCGTCTGGTGTGTCTGGCGAAGTGCTTTTAATGTGTCGA  >  NC_000913/4105299‑4105492

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑