Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,875,075	C→A	A168S (GCG→TCG)	nimR ←	DNA‑binding transcriptional repressor NimR

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,875,075	0	C	A	100.0%	213.0 / NA	61	A168S (GCG→TCG)	nimR	DNA‑binding transcriptional repressor NimR
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (28/33);  total (28/33)

TCAGCTGTAACTGCTGACGCCACTGGCGAAAACTCAACCCCGTCTCTTTTACTATCAGTCGGGCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCACTCGACAGGCCCTTTCGCCATCATCTCCACCATCGTGCGGATTTTAGGATGAGAAGAAACGGGCAGGTGCAGCTGTTGTTGTGGCTGCTGAGGGAGTTCATCAAACAGGACCTGAATTAATCTGCGGGTCATTGGCTCAGCACGCTGAGTCGT  >  NC_000913/1874940‑1875210                                                                                                                                        |                                                                                                                                        tCAGCTGTAACTGCTGACGCCACTGGCGAAAACTCAACCCCGTCTCTTTTACTATCAGTCGGGCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCACTCGACAGGCCCTTTCGAcatc                                                                                                                                     <  1:176141/140‑1 (MQ=255) tCAGCTGTAACTGCTGACGCCACTGGCGAAAACTCAACCCCGTCTCTTTTACTATCAGTCGGGCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCACTCGACAGGCCCTTTCGAcatc                                                                                                                                     <  2:31498/140‑1 (MQ=255) tCAGCTGTAACTGCTGACGCCACTGGCGAAAACTCAACCCCGTCTCTTTTACTATCAGTCGGGCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCACTCGACAGGCCCTTTCGAcatc                                                                                                                                     <  1:682641/140‑1 (MQ=255)   aGCTGTAACTGCTGACGCCACTGGCGAAAACTCAACCCCGTCTCTTTTACTATCAGTCGGGCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCACTCGACAGGCCCTTTCGAcatcat                                                                                                                                   >  2:799499/1‑140 (MQ=255)      tGTAACTGCTGACGCCACTGGCGAAAACTCAACCCCGTCTCTTTTACTATCAGTCGGGCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCACTCGACAGGCCCTTTCGACATCAtctc                                                                                                                                >  2:140065/1‑140 (MQ=255)      tGTAACTGCTGACGCCACTGGCGAAAACTCAACCCCGTCTCTTTTACTATCAGTCGGGCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCACTCGACAGGCCCTTTCGACATCAtctc                                                                                                                                >  2:931283/1‑140 (MQ=255)      tGTAACTGCTGACGCCACTGGCGAAAACTCAACCCCGTCTCTTTTACTATCAGTCGGGCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCACTCGACAGGCCCTTTCGACATCAtctc                                                                                                                                >  2:432957/1‑140 (MQ=255)        tAACTGCTGACGCCACTGGCGAAAACTCAACCCCGTCTCTTTTACTATCAGTCGGGCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCACTCGACAGGCCCTTTCGACATCATCTcca                                                                                                                              >  2:180310/1‑140 (MQ=255)           ctgctgACGCCACTGGCGAAAACTCAACCCCGTCTCTTTTACTATCAGTCGGGCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCACTCGACAGGCCCTTTCGACATCATCTccacca                                                                                                                           <  1:432957/140‑1 (MQ=255)                gACGCCACTGGCGAAAACTCAACCCCGTCTCTTTTACTATCAGTCGGGCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCACTCGACAGGCCCTTTCGACATCATCTCCACCATCGTg                                                                                                                      <  1:291218/140‑1 (MQ=255)                 aCGCCACTGGCGAAAACTCAACCCCGTCTCTTTTACTATCAGTCGGGCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCACTCGACAGGCCCTTTCGACATCATCTCCACCATCGTGc                                                                                                                     <  1:514797/140‑1 (MQ=255)                 aCGCCACTGGCGAAAACTCAACCCCGTCTCTTTTACTATCAGTCGGGCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCACTCGACAGGCCCTTTCGACATCATCTCCACCATCGTGc                                                                                                                     <  1:963921/140‑1 (MQ=255)                 aCGCCACTGGCGAAAACTCAACCCCGTCTCTTTTACTATCAGTCGGGCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCACTCGACAGGCCCTTTCGACATCATCTCCACCATCGTGc                                                                                                                     <  1:477296/140‑1 (MQ=255)                        tGGCGAAAACTCAACCCCGTCTCTTTTACTATCAGTCGGGCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCACTCGACAGGCCCTTTCGACATCATCTCCACCATCGTGCGGAtttt                                                                                                              >  2:617620/1‑140 (MQ=255)                        tGGCGAAAACTCAACCCCGTCTCTTTTACTATCAGTCGGGCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCACTCGACAGGCCCTTTCGACATCATCTCCACCATCGTGCGGAtttt                                                                                                              >  2:587970/1‑140 (MQ=255)                            gAAAACTCAACCCCGTCTCTTTTACTATCAGTCGGGCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCACTCGACAGGCCCTTTCGACATCATCTCCACCATCGTGCGGATTTTAGGa                                                                                                          <  1:931283/140‑1 (MQ=255)                               aaCTCAACCCCGTCTCTTTTACTATCAGTCGGGCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCACTCGACAGGCCCTTTCGACATCATCTCCACCATCGTGCGGATTTTAGGATga                                                                                                       <  1:111360/140‑1 (MQ=255)                                     aCCCCGTCTCTTTTACTATCAGTCGGGCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCACTCGACAGGCCCTTTCGACATCATCTCCACCATCGTGCGGATTTTAGGATGAgaagaa                                                                                                 <  1:561504/140‑1 (MQ=255)                                         cGTCTCTTTTACTATCAGTCGGGCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCACTCGACAGGCCCTTTCGACATCATCTCCACCATCGTGCGGATTTTAGGATGAGAAGAAACgg                                                                                             >  2:745418/1‑140 (MQ=255)                                          gTCTCTTTTACTATCAGTCGGGCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCACTCGACAGGCCCTTTCGACATCATCTCCACCATCGTGCGGATTTTAGGATGAGAAGAAACggg                                                                                            <  2:587194/140‑1 (MQ=255)                                           tctcTTTTACTATCAGTCGGGCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCACTCGACAGGCCCTTTCGACATCATCTCCACCATCGTGCGGATTTTAGGATGAGAAGAAACGGGc                                                                                           <  1:617620/140‑1 (MQ=255)                                              ctTTTACTATCAGTCGGGCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCACTCGACAGGCCCTTTCGACATCATCTCCACCATCGTGCGGATTTTAGGATGAGAAGAAACGGGCAgg                                                                                        <  1:745418/140‑1 (MQ=255)                                                       tCAGTCGGGCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCACTCGACAGGCCCTTTCGACATCATCTCCACCATCGTGCGGATTTTAGGATGAGAAGAAACGGGc                                                                                           <  1:226895/128‑1 (MQ=255)                                                       tCAGTCGGGCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCACTCGACAGGCCCTTTCGACATCATCTCCACCATCGTGCGGATTTTAGGATGAGAAGAAACGGGc                                                                                           >  2:226895/1‑128 (MQ=255)                                                         aGTCGGGCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCACTCGACAGGCCCTTTCGACATCATCTCCACCATCGTGCGGATTTTAGGATGAGAAGAAACGGGCAGGTGCAGCtgttg                                                                             >  1:451017/1‑140 (MQ=255)                                                         aGTCGGGCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCACTCGACAGGCCCTTTCGACATCATCTCCACCATCGTGCGGATTTTAGGATGAGAAGAAACGGGCAGGTGCAGCtgttg                                                                             >  1:346388/1‑140 (MQ=255)                                                           tCGGGCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCACTCGACAGGCCCTTTCGACATCATCTCCACCATCGTGCGGATTTTAGGATGAGAAGAAACGGGCAGGTGCAGCtgttgtt                                                                           >  1:924724/1‑140 (MQ=255)                                                           tCGGGCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCACTCGACAGGCCCTTTCGACATCATCTCCACCATCGTGCGGATTTTAGGATGAGAAGAAACGGGCAGGTGCAGCtgttgtt                                                                           >  1:458593/1‑140 (MQ=255)                                                           tCGGGCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCACTCGACAGGCCCTTTCGACATCATCTCCACCATCGTGCGGATTTTAGGATGAGAAGAAACGGGCAGGTGCAGCtgttgtt                                                                           >  1:201689/1‑140 (MQ=255)                                                              ggCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCACTCGACAGGCCCTTTCGACATCATCTCCACCATCGTGCGGATTTTAGGATGAGAAGAAACGGGCAGGTGc                                                                                     <  1:698700/127‑1 (MQ=255)                                                              ggCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCACTCGACAGGCCCTTTCGACATCATCTCCACCATCGTGCGGATTTTAGGATGAGAAGAAACGGGCAGGTGc                                                                                     >  2:698700/1‑127 (MQ=255)                                                              ggCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCACTCGACAGGCCCTTTCGACATCATCTCCACCATCGTGCGGATTTTAGGATGAGAAGAAACGGGCAGGTGCAGCTGTTGTtgtg                                                                        <  2:563732/140‑1 (MQ=255)                                                              ggCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCACTCGACAGGCCCTTTCGACATCATCTCCACCATCGTGCGGATTTTAGGATGAGAAGAAACGGGCAGGTGCAGCTGTTGTtgtg                                                                        >  1:309067/1‑140 (MQ=255)                                                                cAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCACTCGACAGGCCCTTTCGACATCATCTCCACCATCGTGCGGATTTTAGGATGAGAAGAAACGGGCAGGTGCAGCTGTTGTTGTGgc                                                                      <  1:799499/140‑1 (MQ=255)                                                                 aaGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCACTCGACAGGCCCTTTCGACATCATCTCCACCATCGTGCGGATTTTAGGATGAGAAGAAACGGGCAGGTGCAGCTGTTGTTGTGgct                                                                     <  1:390066/140‑1 (MQ=255)                                                                        cGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCACTCGACAGGCCCTTTCGACATCATCTCCACCATCGTGCGGATTTTAGGATGAGAAGAAACGGGCAGGTGCAGCTGTTGTTGTGGCTGCTGAgg                                                              <  2:955487/140‑1 (MQ=255)                                                                        cGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCACTCGACAGGCCCTTTCGACATCATCTCCACCATCGTGCGGATTTTAGGATGAGAAGAAACGGGCAGGTGCAGCTGTTGTTGTGGCTGCTGAgg                                                              >  1:311034/1‑140 (MQ=255)                                                                        cGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCACTCGACAGGCCCTTTCGACATCATCTCCACCATCGTGCGGATTTTAGGATGAGAAGAAACGGGCAGGTGCAGCTGTTGTTGTGGCTGCTGAgg                                                              <  1:464415/140‑1 (MQ=255)                                                                         gTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCACTCGACAGGCCCTTTCGACATCATCTCCACCATCGTGCGGATTTTAGGATGAGAAGAAACGGGCAGGTGCAGCTGTTGTTGTGGCTGCTGAggg                                                             >  1:953258/1‑140 (MQ=255)                                                                         gTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCACTCGACAGGCCCTTTCGACATCATCTCCACCATCGTGCGGATTTTAGGATGAGAAGAAACGGGCAGGTGCAGCTGTTGTTGTGGCTGCTGAggg                                                             >  1:805126/1‑140 (MQ=255)                                                                          ttCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCACTCGACAGGCCCTTTCGACATCATCTCCACCATCGTGCGGATTTTAGGATGAGAAGAAACGGGCAGGTGCAGCTGTTGTTGTGGCTGCTGAGGGa                                                            <  2:749346/140‑1 (MQ=255)                                                                          ttCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCACTCGACAGGCCCTTTCGACATCATCTCCACCATCGTGCGGATTTTAGGATGAGAAGAAACGGGCAGGTGCAGCTGTTGTTGTGGCTGCTGAGGGa                                                            <  2:201689/140‑1 (MQ=255)                                                                          ttCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCACTCGACAGGCCCTTTCGACATCATCTCCACCATCGTGCGGATTTTAGGATGAGAAGAAACGGGCAGGTGCAGCTGTTGTTGTGGCTGCTGAGGGa                                                            <  2:346388/140‑1 (MQ=255)                                                                             aCTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCACTCGACAGGCCCTTTCGACATCATCTCCACCATCGTGCGGATTTTAGGATGAGAAGAAACGGGCAGGTGCAGCTGTTGTTGTGGCTGCTGAGGGAGt                                                          >  2:390798/1‑139 (MQ=255)                                                                             aCTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCACTCGACAGGCCCTTTCGACATCATCTCCACCATCGTGCGGATTTTAGGATGAGAAGAAACGGGCAGGTGCAGCTGTTGTTGTGGCTGCTGAGGGAGt                                                          <  1:390798/139‑1 (MQ=255)                                                                                   cGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCACTCGACAGGCCCTTTCGACATCATCTCCACCATCGTGCGGATTTTAGGATGAGAAGAAACGGGCAGGTGCAGCTGTTGTTGTGgctg                                                                    >  1:952704/1‑123 (MQ=255)                                                                                   cGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCACTCGACAGGCCCTTTCGACATCATCTCCACCATCGTGCGGATTTTAGGATGAGAAGAAACGGGCAGGTGCAGCTGTTGTTGTGgctg                                                                    <  2:952704/123‑1 (MQ=255)                                                                                       aaaaaGCCAGCCCATTGCCCCAATGCCCCCCACTCGACAGGCCCTTTCGACATCATCTCCACCATCGTGCGGATTTTAGGATGAGAAGAAACGGGCAGGTGCAGCTGTTGTTGTGGCTGCTGAGGGAGTTCATCAAACAg                                               >  1:887154/1‑140 (MQ=255)                                                                                          aaGCCAGCCCATTGCCCCAATGCCCCCCACTCGACAGGCCCTTTCGACATCATCTCCACCATCGTGCGGATTTTAGGATGAGAAGAAACGGGCAGGTGCAGCTGTTGTTGTGGCTGCTGAGGGAGTTCATCAAACAGGAc                                            <  1:787446/140‑1 (MQ=255)                                                                                          aaGCCAGCCCATTGCCCCAATGCCCCCCACTCGACAGGCCCTTTCGACATCATCTCCACCATCGTGCGGATTTTAGGATGAGAAGAAACGGGCAGGTGCAGCTGTTGTTGTGGCTGCTGAGGGAGTTCATCAAACAGGAc                                            <  1:140065/140‑1 (MQ=255)                                                                                             ccagccCATTGCCCCAATGCCCCCCACTCGACAGGCCCTTTCGACATCATCTCCACCATCGTGCGGATTTTAGGATGAGAAGAAACGGGCAGGTGCAGCTGTTGTTGTGGCTGCTGAGGGAGTtcat                                                      >  1:575581/1‑127 (MQ=255)                                                                                             ccagccCATTGCCCCAATGCCCCCCACTCGACAGGCCCTTTCGACATCATCTCCACCATCGTGCGGATTTTAGGATGAGAAGAAACGGGCAGGTGCAGCTGTTGTTGTGGCTGCTGAGGGAGTtcat                                                      <  2:575581/127‑1 (MQ=255)                                                                                                    aTTGCCCCAATGCCCCCCACTCGACAGGCCCTTTCGACATCATCTCCACCATCGTGCGGATTTTAGGATGAGAAGAAACGGGCAGGTGCAGCTGTTGTTGTGGCTGCTGAGGGAGTTCATCAAACAGGACCTGAATTAAt                                  <  1:180310/140‑1 (MQ=255)                                                                                                       gCCCCAATGCCCCCCACTCGACAGGCCCTTTCGACATCATCTCCACCATCGTGCGGATTTTAGGATGAGAAGAAACGGGCAGGTGCAGCTGTTGTTGTGGCTGCTGAGGGAGTTCATCAAACAGGACCTGAATTAATCTg                               <  2:924724/140‑1 (MQ=255)                                                                                                          ccAATGCCCCCCACTCGACAGGCCCTTTCGACATCATCTCCACCATCGTGCGGATTTTAGGATGAGAAGAAACGGGCAGGTGCAGCTGTTGTTGTGGCTGCTGAGGGAGTTCATCAAACAGGACCTGAATTAATCTGCgg                            <  2:887154/140‑1 (MQ=255)                                                                                                              tGCCCCCCACTCGACAGGCCCTTTCGACATCATCTCCACCATCGTGCGGATTTTAGGATGAGAAGAAACGGGCAGGTGCAGCTGTTGTTGTGGCTGCTGAGGGAGTTCATCAAACAGGACCTGAATTAATCTGCGGGTCa                        >  2:518729/1‑140 (MQ=255)                                                                                                                   cccACTCGACAGGCCCTTTCGACATCAACTCCACCATCGTGCGGATTTTAGGATGAGAAGAAACGGGCAGGTGCAGCTGTTGTTGTGGCTGCTGAGGGAGTTCATCAAACAGGACCTGAATTAATCTGCGGGTCATTGGc                   >  2:197809/1‑140 (MQ=255)                                                                                                                               gCCCTTTCGACATCATCTCCACCATCGTGCGGATTTTAGGATGAGAAGAAACGGGCAGGTGCAGCTGTTGTTGTGGCTGCTGAGGGAGTTCATCAAACAGGACCTGAATTAATCTGCGGGTCATTGGCTCAGc              <  1:200353/133‑1 (MQ=255)                                                                                                                               gCCCTTTCGACATCATCTCCACCATCGTGCGGATTTTAGGATGAGAAGAAACGGGCAGGTGCAGCTGTTGTTGTGGCTGCTGAGGGAGTTCATCAAACAGGACCTGAATTAATCTGCGGGTCATTGGCTCAGc              >  2:200353/1‑133 (MQ=255)                                                                                                                               gCCCTTTCGACATCATCTCCACCATCGTGCGGATTTTAGGATGAGAAGAAACGGGCAGGTGCAGCTGTTGTTGTGGCTGCTGAGGGAGTTCATCAAACAGGACCTGAATTAATCTGCGGGTCATTGGCTCAGCACGCTGa       >  1:623745/1‑140 (MQ=255)                                                                                                                                    ttCGACATCATCTCCACCATCGTGCGGATTTTAGGATGAGAAGAAACGGGCAGGTGCAGCTGTTGTTGTGGCTGCTGAGGGAGTTCATCAAACAGGACCTGAATTAATCTGCGGGTCATTGGCTCAGCACGCTGAgtcgt  >  2:632273/1‑140 (MQ=255)                                                                                                                                        |                                                                                                                                        TCAGCTGTAACTGCTGACGCCACTGGCGAAAACTCAACCCCGTCTCTTTTACTATCAGTCGGGCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCACTCGACAGGCCCTTTCGCCATCATCTCCACCATCGTGCGGATTTTAGGATGAGAAGAAACGGGCAGGTGCAGCTGTTGTTGTGGCTGCTGAGGGAGTTCATCAAACAGGACCTGAATTAATCTGCGGGTCATTGGCTCAGCACGCTGAGTCGT  >  NC_000913/1874940‑1875210

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑