Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,823,036	A→C	I213L (ATC→CTC)	spoT →	bifunctional (p)ppGpp synthetase II/ guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,823,036	0	A	C	100.0%	219.3 / NA	54	I213L (ATC→CTC)	spoT	bifunctional (p)ppGpp synthetase II/ guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base C (25/29);  total (25/29)

TTATAGCCCGCTGGCGCACCGTTTAGGTATCCACCACATTAAAACCGAACTCGAAGAGCTGGGTTTTGAGGCGCTGTATCCCAACCGTTATCGCGTAATCAAAGAAGTGGTGAAAGCCGCGCGCGGCAACCGTAAAGAGATGATCCAGAAGATTCTTTCTGAAATCGAAGGGCGTTTGCAGGAAGCGGGAATACCGTGCCGCGTCAGTGGTCGCGAGAAGCATCTTTATTCGATTTACTGCAAAATGGTGCTCAAAGAGCAGCGTTTTCACTCGATCATGGACATCT  >  NC_000913/3822894‑3823180                                                                                                                                               |                                                                                                                                                 ttATAGCCCGCTGGCGCACCGTTTAGGTATCCACCACATTAAAACCGAACTCGAAGAGCTGGGTTTTGAGGCGCTGTATCCCAACCGTTATCGCGTAATCAAAGAAGTGGTGAAAGCCGCGCGCGGCAACCGTAAAGAGATGCTCCaga                                                                                                                                            >  2:725918/1‑149 (MQ=255)     aGCCCGCTGGCGCACCGTTTAGGTATCCACCACATTAAAACCGAACTCGAAGAGCTGGGTTTTGAGGCGCTGTATCCCAACCGTTATCGCGTAATCAAAGAAGTGGTGAAAGCCGCGCGCGGCAACCGTAAAGAGATGCTCCAGAAGAtt                                                                                                                                       <  2:217041/150‑1 (MQ=255)      gCCCGCTGGCGCACCGTTTAGGTATCCACCACATTAAAACCGAACTCGAAGAGCTGGGTTTTGAGGCGCTGTATCCCAACCGTTATCGCGTAATCAAAGAAGTGGTGAAAGCCGCGCGCGGCAACCGTAAAGAGATGCTCCAGAAGAttct                                                                                                                                     <  1:281286/151‑1 (MQ=255)          gCTGGCGCACCGTTTAGGTATCCACCACATTAAAACCGAACTCGAAGAGCTGGGTTTTGAGGCGCTGTATCCCAACCGTTATCGCGTAATCAAAGAAGTGGTGAAAGCCGCGCGCGGCAACCGTAAAGAGATGCTCCAGAAGAttctttct                                                                                                                                 <  2:127709/151‑1 (MQ=255)              gcgcACCGTTTAGGTATCCACCACATTAAAACCGAACTCGAAGAGCTGGGTTTTGAGGCGCTGTATCCCAACCGTTATCGCGTAATCAAAGAAGTGGTGAAAGCCGCGCGCGGCAACCGTAAAGAGATGCTCCAGAAGATTCTTTCTGaa                                                                                                                              >  2:524175/1‑150 (MQ=255)                       ttAGGTATCCACCACATTAAAACCGAACTCGAAGAGCTGGGTTTTGAGGCGCTGTATCCCAACCGTTATCGCGTAATCAAAGAAGTGGTGAAAGCCGCGCGCGGCAACCGTAAAGAGATGCTCCAGAAGATTCTTTCTGAAATCGAAGGGc                                                                                                                    >  1:435258/1‑151 (MQ=255)                         aGGTATCCACCACATTAAAACCGAACTCGAAGAGCTGGGTTTTGAGGCGCTGTATCCCAACCGTTATCGCGTAATCAAAGAAGTGGTGAAAGCCGCGCGCGGCAACCGTAAAGAGATGCTCCAGAAGATTCTTTCTGAAATCGAAGGGCg                                                                                                                   <  1:23984/150‑1 (MQ=255)                            tATCCACCACATTAAAACCGAACTCGAAGAGCTGGGTTTTGAGGCGCTGTATCCCAACCGTTATCGCGTAATCAAAGAAGTGGTGAAAGCCGCGCGCGGCAACCGTAAAGAGATGCTCCAGAAGATTCTTTCTGAAATCGAAGGGCGTTTg                                                                                                               >  2:512837/1‑151 (MQ=255)                             aTCCACCACATTAAAACCGAACTCGAAGAGCTGGGTTTTGAGGCGCTGTATCCCAACCGTTATCGCGTAATCAAAGAAGGGGTGAAAGCCGCGCGCGGCAACCGTAAAGAGATGCTCCAGAAGATTCTTTCTGAAATCGAAGGGCGt                                                                                                                  >  1:524846/1‑147 (MQ=255)                               ccaccaCATTAAAACCGAACTCGAAGAGCTGGGTTTTGAGGCGCTGTATCCCAACCGTTATCGCGTAATCAAAGAAGTGGTGAAAGCCGCGCGCGGCAACCGTAAAGAGATGCTCCAGAAGATTCTTTCTGAAATCGAAGGGCGTTTGCAg                                                                                                            <  1:676274/151‑1 (MQ=255)                                    acaTTAAAACCGAACTCGAAGAGCTGGGTTTTGAGGCGCTGTATCCCAACCGTTATCGCGTAATCAAAGAAGTGGTGAAAGCCGCGCGCGGCAACCGTAAAGAGATGCTCCAGAAGATTCTTTCTGAAATCGAAGGGCGTTTGCAGGAAGc                                                                                                       <  1:432971/151‑1 (MQ=255)                                          aaaCCGAACTCGAAGAGCTGGGTTTTGAGGCGCTGTATCCCAACCGTTATCGCGTAATCAAAGAAGTGGTGAAAGCCGCGCGCGGCAACCGTAAAGAGATGCTCCAGAAGATTCTTTCTGAAATCGAAGGGCGTTTGCAGGAAGCGGGAAt                                                                                                 <  2:221833/151‑1 (MQ=255)                                           aaCCGAACTCGAAGAGCTGGGTTTTGAGGCGCTGTATCCCAACCGTTATCGCGTAATCAAAGAAGTGGTGAAAGCCGCGCGCGGCAACCGTAAAGAGATGCTCCAGAAGATTCTTTCTGAAATCGAAGGGCGTTTGCAGGAAGCGGGAAt                                                                                                 >  1:462981/1‑150 (MQ=255)                                            aCCGAACTCGAAGAGCTGGGTTTTGAGGCGCTGTATCCCAACCGTTATCGCGTAATCAAAGAAGTGGTGAAAGCCGCGCGCGGCAACCGTAAAGAGATGCTCCAGAAGATTCTTTCTGAAATCGAAGGGCGTTTGCAGGAAGCGGGAATAc                                                                                               >  1:670375/1‑151 (MQ=255)                                                   tCGAAGAGCTGGGTTTTGAGGCGCTGTATCCCAACCGTTATCGCGTAATCAAAGAAGTGGTGAAAGCCGCGCGCGGCAACCGTAAAGAGATGCTCCAGAAGATTCTTTCTGAAATCGAAGGGCGTTTGCAGGAAGCGGGAATACCGTGCcg                                                                                        >  1:714665/1‑151 (MQ=255)                                                    cGAAGAGCTGGGTTTTGAGGCGCTGTATCCCAACCGTTATCGCGTAATCAAAGAAGTGGTGAAAGCCGCGCGCGGCAACCGTAAAGAGATGCTCCAGAAGATTCTTTCTGAAATCGAAGGGCGTTTGCAGGAAGCGGGAATACCGTGCcgc                                                                                       <  2:539776/151‑1 (MQ=255)                                                    cGAAGAGCTGGGTTTTGAGGCGCTGTATCCCAACCGTTATCGCGTAATCAAAGAAGTGGTGAAAGCCGCGCGCGGCAACCGTAAAGAGATGCTCCAGAAGATTCTTTCTGAAATCGAAGGGCGTTTGCAGGAAGCGGGAATACCGTGCcg                                                                                        <  1:235294/150‑1 (MQ=255)                                                      aaGAGCTGGGTTTTGAGGCGCTGTATCCCAACCGTTATCGCGTAATCAAAGAAGTGGTGAAAGCCGCGCGCGGCAACCGTAAAGAGATGCTCCAGAAGATTCTTTCTGAAATCGAAGGGCGTTTGCAGGAAGCGGGAATACCGTGCCGCGt                                                                                     >  1:555252/1‑151 (MQ=255)                                                       agagCTGGGTTTTGAGGCGCTGTATCCCAACCGTTATCGCGTAATCAAAGAAGTGGTGAAAGCCGCGCGCGGCAACCGTAAAGAGATGCTCCAGAAGATTCTTTCTGAAATCGAAGGGCGTTTGCAGGAAGCGGGAATACCGTGCCGCGTc                                                                                    >  2:611107/1‑151 (MQ=255)                                                        gagCTGGGTTTTGAGGCGCTGTATCCCAACCGTTATCGCGTAATCAAAGAAGTGGTGAAAGCCGCGCGCGGCAACCGTAAAGAGATGCTCCAGAAGATTCTTTCTGAAATCGAAGGGCGTTTGCAGGAAGCGGGAATACCGTGCCGCGTCa                                                                                   <  1:420015/151‑1 (MQ=255)                                                           cTGGGTTTTGAGGCGCTGTATCCCAACCGTTATCGCGTAATCAAAGAAGTGGTGAAAGCCGCGCGCGGCAACCGTAAAGAGATGCTCCAGAAGATTCTTTCTGAAATCGAAGGGCGTTTGCAGGAAGCGGGAATACCGTGCCGCGTCAGTg                                                                                >  1:768783/1‑151 (MQ=255)                                                              ggTTTTGAGGCGCTGTATCCCAACCGTTATCGCGTAATCAAAGAAGTGGTGAAAGCCGCGCGCGGCAACCGTAAAGAGATGCTCCAGAAGATTCTTTCTGAAATCGAAGGGCGTTTGCAGGAAGCGGGAATACCGTGCCGCGTCAGTGGTc                                                                             <  1:518044/151‑1 (MQ=255)                                                                 tttGAGGCGCTGTATCCCAACCGTTATCGCGTAATCAAAGAAGTGGTGAAAGCCGCGCGCGGCAACCGTAAAGAGATGCTCCAGAAGATTCTTTCTGAAATCGAAGGGCGTTTGCAGGAAGCGGGAATACCGTGCCGCGTCAGTGGTcgc                                                                           <  1:751916/150‑1 (MQ=255)                                                                   tGAGGCGCTGTATCCCAACCGTTATCGCGTAATCAAAGAAGTGGTGAAAGCCGCGCGCGGCAACCGTAAAGAGATGCTCCAGAAGATTCTTTCTGAAATCGAAGGGCGTTTGCAGGAAGCGGGAATACCGTGCCGCGTCAGTGGTcgcg                                                                          >  2:747199/1‑149 (MQ=255)                                                                    gAGGCGCTGTATCCCAACCGTTATCGCGTAATCAAAGAAGTGGTGAAAGCCGCGCGCGGCAACCGTAAAGAGATGCTCCAGAAGATTCTTTCTGAAATCGAAGGGCGTTTGCAGGAAGCGGGAATACCGTGCCGCGTCAGTGGTCGCgaga                                                                       <  2:277358/151‑1 (MQ=255)                                                                      ggCGCTGTATCCCAACCGTTATCGCGTAATCAAAGAAGTGGTGAAAGCCGCGCGCGGCAACCGTAAAGAGATGCTCCAGAAGATTCTTTCTGAAATCGAAGGGCGTTTGCAGGAAGCGGGAATACCGTGCCGCGTCAGTGGTCGCgaga                                                                       >  1:420224/1‑149 (MQ=255)                                                                      ggCGCTGTATCCCAACCGTTATCGCGTAATCAAAGAAGTGGTGAAAGCCGCGCGCGGCAACCGTAAAGAGATGCTCCAGAAGATTCTTTCTGAAATCGAAGGGCGTTTGCAGGAAGCGGGAATACCGTGCCGCGTCAGTGGTCGCGAGAAg                                                                     <  1:604603/151‑1 (MQ=255)                                                                       gcgcTGTATCCCAACCGTTATCGCGTAATCAAAGAAGTGGTGAAAGCCGCGCGCGGCAACCGTAAAGAGATGCTCCAGAAGATTCTTTCTGAAATCGAAGGGCGTTTGCAGGAAGCGGGAATACCGTGCCGCGTCAGTGGTCGCGAGAAGc                                                                    <  2:414018/151‑1 (MQ=255)                                                                            gTATCCCAACCGTTATCGCGTAATCAAAGAAGTGGTGAAAGCCGCGCGCGGCAACCGTAAAGAGATGCTCCAGAAGATTCTTTCTGAAATCGAAGGGCGTTTGCAGGAAGCGGGAATACCGTGCCGCGTCAGTGGTCGCGAGAAGCATCt                                                                <  2:21336/150‑1 (MQ=255)                                                                              aTCCCAACCGTTATCGCGTAATCAAAGAAGTGGTGAAAGCCGCGCGCGGCAACCGTAAAGAGATGCTCCAGAAGATTCTTTCTGAAATCGAAGGGCG‑TTGCAGGAAGCGGGAATACCGTGCCGCGGCAGTGGTCGCGAGAAGCATCTTTAt                                                            <  2:325496/151‑1 (MQ=255)                                                                                cccAACCGTTATCGCGTAATCAAAGAAGTGGTGAAAGCCGCGCGCGGCAACCGTAAAGAGATGCTCCAGAAGATTCTTTCTGAAATCGAAGGGCGTTTGCAGGAAGCGGGAATACCGTGCCGCGTCAGTGGTCGCGAGAAGCATCTTTAtt                                                           >  2:307996/1‑151 (MQ=255)                                                                                cccAACCGTTATCGCGTAATCAAAGAAGTGGTGAAAGCCGCGCGCGGCAACCGTAAAGAGATGCTCCAGAAGATTCTTTCTGAAATCGAAGGGCGTTTGCAAGAAGCGGGAATACCGTGCCGCGTCAGTGGTCGCGAGAAGCATCTTTAtt                                                           <  2:329675/151‑1 (MQ=255)                                                                                 ccAACCGTTATCGCGTAATCAAAGAAGTGGTGAAAGCCGCGCGCGGCAACCGTAAAGAGATGCTCCAGAAGATTCTTTCTGAAATCGAAGGGCGTTTGCAGGAAGCGGGAATACCGTGCCGCGTCAGTGGTCGCGAGAAGCATCTTTATTc                                                          <  2:555198/151‑1 (MQ=255)                                                                                   aaCCGTTATCGCGTAATCAAAGAAGTGGTGAAAGCCGCGCGCGGCAACCGTAAAGAGATGCTCCAGAAGATTCTTTCTGAAATCGAAGGGCGTTTGCAGGAAGCGGGAATACCGTGCCGCGTCAGTGGTCGCGAGAAGCATCTTTATTCg                                                         >  2:536881/1‑150 (MQ=255)                                                                                   aaCCGTTATCGCGTAATCAAAGAAGTGGTGAAAGCCGCGCGCGGCAACCGTAAAGAGATGCTCCAGAAGATTCTTTCTGAAATCGAAGGGCGTTTGCAGGAAGCGGGAATACCGTGCCGCGTCAGTGGTCGCGAGAAGCATCTTTATTCg                                                         >  2:23464/1‑150 (MQ=255)                                                                                    aCCGTTATCGCGTAATCAAAGAAGTGGTGAAAGCCGCGCGCGGCAACCGTAAAGAGATGCTCCAGAAGATTCTTTCTGAAATCGAAGGGCGTTTGCAGGAAGCGGGAATACCGTGCCGCGTCAGTGGTCGCGAGAAGCATCTTTATTCGAt                                                       >  1:65186/1‑151 (MQ=255)                                                                                               gTAATCAAAGAAGTGGTGAAAGCCGCGCGCGGCAACCGTAAAGAGATGCTCCAGAAGATTCTTTCTGAAATCGAAGGGCGTTTGCAGGAAGCGGGAATACCGTGCCGCGTCAGTGGTCGCGAGAAGCATCTTTATTCGATTTACTGCaaaa                                            <  2:262648/151‑1 (MQ=255)                                                                                                tAATCAAAGAAGTGGTGAAAGCCGCGCGCGGCAACCGTAAAGAGATGCTCCAGAAGATTCTTTCTGAAATCGAAGGGCGTTTGCAGGAAGCGGGAATACCGTGCCGCGTCAGTGGTCGCGAGAAGCATCTTTATTCGAtt                                                      >  2:763995/1‑140 (MQ=255)                                                                                                tAATCAAAGAAGTGGTGAAAGCCGCGCGCGGCAACCGTAAAGAGATGCTCCAGAAGATTCTTTCTGAAATCGAAGGGCGTTTGCAGGAAGCGGGAATACCGTGCCGCGTCAGTGGTCGCGAGAAGCATCTTTATTCGAtt                                                      <  1:764061/140‑1 (MQ=255)                                                                                                  aTCAAAGAAGTGGTGAAAGCCGCGCGCGGCAACCGTAAAGAGATGCTCCAGAAGATTCTTTCTGAAATCGAAGGGCGTTTGCAGGAAGCGGGAATACCGTGCCGCGTCAGTGGTCGCGAGAAGCATCTTTATTCGATTTACTGCAAAATgg                                         >  2:704321/1‑151 (MQ=255)                                                                                                    cAAAGAAGTGGTGAAAGCCGCGCGCGGCAACCGTAAAGAGATGCTCCAGAAGATTCTTTCTGAAATCGAAGGGCGTTTGCAGGAAGCGGGAATACCGTGCCGCGTCAGTGGTCGCGAGAAGCATCTTTATTCGATTTACTGCAAAATGGTg                                       <  2:19978/151‑1 (MQ=255)                                                                                                       agaagTGGTGAAAGCCGCGCGCGGCAACCGTAAAGAGATGCTCCAGAAGATTCTTTCTGAAATCGAAGGGCGTTTGCAGGAAGCGGGAATACCGTGCCGCGTCAGTGGTCGCGAGAAGCATCTTTATTCGATTTACTGCAAAATGGTGCTc                                    >  2:269485/1‑151 (MQ=255)                                                                                                                gAAAGCCGCGCGCGGCAACCGTAAAGAGATGCTCCAGAAGATTCTTTCTGAAATCGAAGGGCGTTTGCAGGAAGCGGGAATACCGTGCCGCGTCAGTGGTCGCGAGAAGCATCTTTATTCGATTTACTGCAAAATGGTGCTCAAAGagc                             >  2:307680/1‑149 (MQ=255)                                                                                                                  aaGCCGCGCGCGGCAACCGTAAAGAGATGCTCCAGAAGATTCTTTCTGAAATCGAAGGGCGTTTGCAGGAAGCGGGAATACCGTGCCGCGTCAGTGGTCGCGAGAAGCATCTTTATTCGATTTACTGCAAAATGGTGCTCAAAGAGCAGCg                         <  2:295297/151‑1 (MQ=255)                                                                                                                  aaGCCGCGCGCGGCAACCGTAAAGAGATGCTCCAGAAGATTCTTTCTGAAATCGAAGGGCGTTTGCAGGAAGCGGGAATACCGTGCCGCGTCAGTGGTCGCGAGAAGCATCTTTATTCGATTTACTGCAAAATGGTGCTCAAAGAGCAGCg                         >  1:608683/1‑151 (MQ=255)                                                                                                                  aaGCCGCGCGCGGCAACCGTAAAGAGATGCTCCAGAAGATTCTTTCTGAAATCGAAGGGCGTTTGCAGGAAGCGGGAATACCGTGCCGCGTCAGTGGTCGCGAGAAGCATCTTTATTCGATTTACTGCAAAATGGTGCTCAAAGAGCAGCg                         <  1:339342/151‑1 (MQ=255)                                                                                                                  aaGCCGCGCGCGGCAACCGTAAAGAGATGCTCCAGAAGATTCTTTCTGAAATCGAAGGGCGTTTGCAGGAAGCGGGAATACCGTGCCGCGTCAGTGGTCGCGAGAAGCATCTTTATTCGATTTACTGCAAAATGGTGCTCAAAGAGCAGCg                         >  1:407828/1‑151 (MQ=255)                                                                                                                    gCCGCGCGCGGCAACCGTAAAGAGATGCTCCAGAAGATTCTTTCTGAAATCGAAGGGCGTTTGCAGGAAGCGGGAATACCGTGCCGCGTCAGTGGTCGCGAGAAGCATCTTTATTCGATTTACTGCAAAATGGTGCTCAAAGAGCAGCGtt                       <  2:331524/151‑1 (MQ=255)                                                                                                                             ggCAACCGTAAAGAGATGCTCCAGAAGATTCTTTCTGAAATCGAAGGGCGTTTGCAGGAAGCGGGAATACCGTGCCGCGTCAGTGGTCGCGAGAAGCATCTTTATTCGATTTACTGCAAAATGGTGCTCAAAGAGCAGCGTTTTCACTCg               >  2:167791/1‑150 (MQ=255)                                                                                                                                    gTAAAGAGATGCTCCAGAAGATTCTTTCTGAAATCGAAGGGCGTTTGCAGGAAGCGGGAATACCGTGCCGCGTCAGTGGTCGCGAGAAGCATCTTTATTCGATTTACTGCAAAATGGTGCTCAAAGAGCAGCGTTTTCACTCGATCATGGa       <  2:665072/151‑1 (MQ=255)                                                                                                                                      aaaGAGATGCTCCAGAAGATTCTTTCTGAAATCGAAGGGCGTTTGCAGGAAGCGGGAATACCGTGCCGCGTCAGTGGTCGCGAGAAGCATCTTTATTCGATTTACTGCAAAATGGTGCTCAAAGAGCAGCGTTTTCACTCGATCATGGAc      <  1:725983/150‑1 (MQ=255)                                                                                                                                       aaGAGATGCTCCAGAAGATTCTTTCTGAAATCGAAGGGCGTTTGCAGGAAGCGGGAATACCGTGCCGCGTCAGTGGTCGCGAGAAGCATCTTTATTCGATTTACTGCAAAATGGTGCTCAAAGAGCAGCGTTTTCACTCGATCATGGACAt    >  2:445169/1‑151 (MQ=255)                                                                                                                                         gagaTGCTCCAGAAGATTCTTTCTGAAATCGAAGGGCGTTTGCAGGAAGCGGGAATACCGTGCCGCGTCAGTGGTCGCGAGAAGCATCTTTATTCGATTTACTGCAAAATGGTGCTCAAAGAGCAGCGTTTTCACTCGATCATGGACATCt  <  2:47801/151‑1 (MQ=255)                                                                                                                                         gagaTGCTCCAGAAGATTCTTTCTGAAATCGAAGGGCGTTTGCAGGAAGCGGGAATACCGTGCCGCGTCAGTGGTCGCGAGAAGCATCTTTATTCGATTTACTGCAAAATGGTGCTCAAAGAGCAGCGTTTTCACTCGATCATGGACATCt  <  2:816579/151‑1 (MQ=255)                                                                                                                                               |                                                                                                                                                 TTATAGCCCGCTGGCGCACCGTTTAGGTATCCACCACATTAAAACCGAACTCGAAGAGCTGGGTTTTGAGGCGCTGTATCCCAACCGTTATCGCGTAATCAAAGAAGTGGTGAAAGCCGCGCGCGGCAACCGTAAAGAGATGATCCAGAAGATTCTTTCTGAAATCGAAGGGCGTTTGCAGGAAGCGGGAATACCGTGCCGCGTCAGTGGTCGCGAGAAGCATCTTTATTCGATTTACTGCAAAATGGTGCTCAAAGAGCAGCGTTTTCACTCGATCATGGACATCT  >  NC_000913/3822894‑3823180

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑