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	98.7%	263.3 / ‑3.9	76	L92Q (CTG→CAG)	cpxR	response regulator in two‑component regulatory system with CpxA
Reads supporting (aligned to +/- strand):  ref base A (0/1);  new base T (35/40);  total (35/41)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.87e-01

CTGTTGCTCGCTCCAGTGCGAACGGCGCAGGATCGCGCGAATACGTGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCAGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACAGGCGTCTGGTGTGTCTGGCGAAGTGCTTTTAATGTGTCG  >  NC_000913/4105299‑4105491                                                                                                  |                                                                                                cTGTTGCTCGCTCCAGTGCGAACGGCGCAGGATCGCGCGAATACGTGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGc                                                                                               <  1:611049/100‑1 (MQ=255)      gctcgctcCAGTGCGAACGGCGCAGGATCGCGCGAATACGTGCCGCCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAg                                                                                          >  2:733957/1‑100 (MQ=255)      gctcgctcCAGTGCGAACGGCGCAGGATCGCGCGAATACGTGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAg                                                                                          >  2:41222/1‑100 (MQ=255)       ctcgctcCAGTGCGAACGGCGCAGGATCGCGCGAATACGTGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAgg                                                                                         >  2:1832957/1‑100 (MQ=255)        tcgctcCAGTGCGAACGGCGCAGGATCGCGCGAATACGTGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGc                                                                                        >  2:784229/1‑100 (MQ=255)        tcgctcCAGTGCGAACGGCGCAGGATCGCGCGAATACGTGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGc                                                                                        <  2:58840/100‑1 (MQ=255)         cgctcCAGTGTGAACGGCGCAGGATCGCGCGAATACGTGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGcc                                                                                       >  2:1391688/1‑100 (MQ=255)         cgctcCAGTGCGAACGGCGCAGGATCGCGCGAATACGTGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGcc                                                                                       <  1:234639/100‑1 (MQ=255)          gctcCAGTGCGAACGGCGCAGGATCGCGCGAATACGTGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCg                                                                                      <  1:1685199/100‑1 (MQ=255)          gctcCAGTGCGAACGGCGCAGGATCGCGCGAATACGTGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCAGCTCAAGGCCg                                                                                      <  1:1437715/100‑1 (MQ=255)            tcCAGTGCGAACGGCGCAGGATCGCGCGAATACGTGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCgag                                                                                    <  1:1567218/100‑1 (MQ=255)                gTGCGAACGGCGCAGGATCGCGCGAATACGTGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAAcg                                                                                >  2:1027303/1‑100 (MQ=255)                 tGCGAACGGCGCAGGATCGCGCGAATACGTGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAAcgc                                                                               <  1:850872/100‑1 (MQ=255)                   cGAACGGCGCAGGATCGCGCGAATACGTGCCACCGGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGa                                                                             >  2:343671/1‑100 (MQ=255)                    gAACGGCGCAGGATCGCGCGAATACGTGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGAt                                                                            >  2:1467614/1‑100 (MQ=255)                    gAACGGCGCAGGATCGCGCGAATACGTGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGAt                                                                            <  2:929077/100‑1 (MQ=255)                        ggCGCAGGATCGCGCGAATACGTGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAg                                                                        <  1:1137517/100‑1 (MQ=255)                         gcgcAGGATCGCGCGAATACGTGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGt                                                                       <  1:1237584/100‑1 (MQ=255)                              ggATCGCGCGAATACGTGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACt                                                                  >  2:1695670/1‑100 (MQ=255)                              ggATCGCGCGAATACGTGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACt                                                                  >  2:1605172/1‑100 (MQ=255)                              ggATCGCGCGAATACGTGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACt                                                                  <  1:1389536/100‑1 (MQ=255)                                aTCGCGCGAATACGTGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGc                                                                <  2:386953/100‑1 (MQ=255)                                    cgcgAATACGTGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCcgcg                                                            >  1:1529532/1‑100 (MQ=255)                                    cgcgAATACGTGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCcgcg                                                            >  2:1316303/1‑100 (MQ=255)                                    cgcgAATACGTGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCcgcg                                                            >  1:1529803/1‑100 (MQ=255)                                      cgAATACGTGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCcgcgcg                                                          <  2:1529794/100‑1 (MQ=255)                                      cgAATACGTGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCcgcgcg                                                          <  2:1529523/100‑1 (MQ=255)                                      cgAATACGTGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCcgcgcg                                                          >  2:820488/1‑100 (MQ=255)                                        aaTACGTGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGcc                                                        <  2:370939/100‑1 (MQ=255)                                         aTACGTGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCg                                                       <  1:211290/100‑1 (MQ=255)                                          tACGTGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGt                                                      >  2:1108164/1‑100 (MQ=255)                                           aCGTGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTc                                                     >  2:792085/1‑100 (MQ=255)                                            cGTGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCa                                                    >  1:1590847/1‑100 (MQ=255)                                              tGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAAc                                                  >  1:174456/1‑100 (MQ=255)                                              tGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAAc                                                  <  2:419914/100‑1 (MQ=255)                                              tGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAAc                                                  <  1:1870499/100‑1 (MQ=255)                                               gCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACa                                                 >  2:1510160/1‑100 (MQ=255)                                               gCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACa                                                 >  1:815886/1‑100 (MQ=255)                                               gCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCCAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACa                                                 <  2:1098271/100‑1 (MQ=255)                                                ccaccaGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACAt                                                >  2:1596482/1‑100 (MQ=255)                                                  accaGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATaa                                              <  1:771523/100‑1 (MQ=255)                                                   ccaGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAAt                                             <  2:525247/100‑1 (MQ=255)                                                         cACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACAgg                                       >  1:1254972/1‑100 (MQ=255)                                                          aCGATCATTAACCGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGTCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACAGGc                                      <  2:399953/100‑1 (MQ=255)                                                          aCGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACAGGc                                      <  2:599528/100‑1 (MQ=255)                                                           cGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACAGGCg                                     >  2:290606/1‑100 (MQ=255)                                                           cGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACAGGCg                                     <  1:504678/100‑1 (MQ=255)                                                                aTTAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACAGGCGTCTgg                                <  2:42800/100‑1 (MQ=255)                                                                 ttAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACAGGCGTCTGgt                               >  1:944109/1‑100 (MQ=255)                                                                 ttAAACGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACAGGCGTCTGgt                               >  2:355285/1‑100 (MQ=255)                                                                   aaaCGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACAGGCGTCTGgtgt                             >  2:1877115/1‑100 (MQ=255)                                                                     aCGGTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACAGGCGTCTGgtgtgt                           >  2:2024052/1‑100 (MQ=255)                                                                       ggTTTCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACAGGCGTCTGGTGTGTCt                         <  1:1391697/100‑1 (MQ=255)                                                                           tCGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACAGGCGTCTGGTGTGTCTGGCg                     <  1:1108169/100‑1 (MQ=255)                                                                           cttccgatctgTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACAGGCGTCTGGTGTGTCTGGCg                     <  2:1435627/90‑1 (MQ=255)                                                                            cGGGAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACACGCGTCTGGTGTGTCTGGCGa                    <  1:1919016/100‑1 (MQ=255)                                                                             gggAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACAGGCGTCTGGTGTGTCTGGCGaa                   >  1:1096448/1‑100 (MQ=255)                                                                             gggAGATAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACAGGCGTCTGGTGTGTCTGGCGaa                   <  1:889583/100‑1 (MQ=255)                                                                               gagaTAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACAGGCGTCTGGTGTGTCTGGCGAAGt                 >  1:1445736/1‑100 (MQ=255)                                                                                 gaTAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACAGGCGTCTGGTGTGTCTGGCGAAGTGc               <  1:343672/100‑1 (MQ=255)                                                                                 gaTAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACAGGCGTCTGGTGTGTCTGGCGAAGTGc               >  2:1853769/1‑100 (MQ=255)                                                                                  aTAGTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACAGGCGTCTGGTGTGTCTGGCGAAGTGCt              <  1:41222/100‑1 (MQ=255)                                                                                     gTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATCATGACAGGCGTCTGGTGTGTCTGGCGagatcggaag           >  1:1435636/1‑91 (MQ=255)                                                                                     gTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACAGGCGTCTGGTGTGTCTGGCGAAGTGCtttt           >  1:993550/1‑100 (MQ=255)                                                                                     gTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACAGGCGTCTGGTGTGTCTGGCGAAGTGCtttt           >  2:1317482/1‑100 (MQ=255)                                                                                     gTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACAGGCGTCTGGTGTGTCTGGCGAAGTGCtttt           >  1:1267389/1‑100 (MQ=255)                                                                                     gTCATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACAGGCGTCTGGTGTGTCTGGCGAAGTGCtttt           <  1:1316311/100‑1 (MQ=255)                                                                                       cATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACAGGCGTCTGGTGTGTCTGGCGAAGTGCTTTTaa         <  1:714961/100‑1 (MQ=255)                                                                                       cATCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACAGGCGTCTGGTGTGTCTGGCGAAGTGCTTTTaa         >  2:1047528/1‑100 (MQ=255)                                                                                        aTCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACAGGCGTCTGGTGTGTCTGGCGAAGTGCTTTTAAt        <  1:565439/100‑1 (MQ=255)                                                                                        aTCTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACAGGCGTCTGGTGTGTCTGGCGAAGTGCTTTTAAt        <  1:1605184/100‑1 (MQ=255)                                                                                          cTGCGCCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACAGGCGTCTGGTGTGTCTGGCGAAGTGCTTTTAAtgt      <  1:1968/100‑1 (MQ=255)                                                                                             cgcCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACAGGCGTCTGGTGTGTCTGGCGAAGTGCTTTTAATGTGTc   <  2:174455/100‑1 (MQ=255)                                                                                             cgcCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACAGGCGTCTGGTGTGTCTGGCGAAGTGCTTTTAATGTGTc   <  1:1343526/100‑1 (MQ=255)                                                                                             cgcCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACAGGCGTCTGGTGTGTCTGGCGAAGTGCTTTTAATGTGTc   <  1:1832973/100‑1 (MQ=255)                                                                                              gcCCTGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACAGGCGTCTGGTGTGTCTGGCGAAGTGCTTTTAATGTGTCg  <  1:1877132/100‑1 (MQ=255)                                                                                                  |                                                                                                CTGTTGCTCGCTCCAGTGCGAACGGCGCAGGATCGCGCGAATACGTGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCAGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACAGGCGTCTGGTGTGTCTGGCGAAGTGCTTTTAATGTGTCG  >  NC_000913/4105299‑4105491

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: ‑