Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,823,759	A→C	N454H (AAT→CAT)	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	3,823,759	0	A	C	100.0%	198.4 / NA	52	N454H (AAT→CAT)	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 (17/35);  total (17/35)

AACGCCCGTCGACTTCGCTTATGCAGTGCATACCGATATCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTGGGCCGTCGTCTGCTCAACCATGCTTTGGGTGGTAGCCGTAAGCTGAATGA  >  NC_000913/3823611‑3823904                                                                                                                                                     |                                                                                                                                                  aaCGCCCGTCGACTTCGCTTATGCAGTGCATACCGATATCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGCAt                                                                                                                                                 <  2:148469/151‑1 (MQ=255)      ccGTCGACTTCGCTCATGCAGTGCATACCGATATCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGCATGCCGc                                                                                                                                            >  1:669664/1‑151 (MQ=255)       cGTCGACTTCGCTTATGCAGTGCATACCGATATCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGCATGCCGCt                                                                                                                                           >  1:599588/1‑151 (MQ=255)        gTCGACTTCGCTTATGCAGTGCATACCGATATCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGCATGCCGCtt                                                                                                                                          <  1:177984/151‑1 (MQ=255)          cGACTTCGCTTATGCAGTGCATACCGATATCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGCATGCCGCTTg                                                                                                                                         <  2:542915/150‑1 (MQ=255)           gACTTCGCTTATGCAGTGCATACCGATATCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGCATGCCGCTTGGc                                                                                                                                       <  1:213147/151‑1 (MQ=255)             cTTCGCTTATGCAGTGCATACCGATATCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGCATGCCGCTTGGCTg                                                                                                                                     >  1:466684/1‑151 (MQ=255)                     aTGCAGTGCATACCGATATCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGCATGCCGCTTGGCTGAACttt                                                                                                                               <  2:13366/149‑1 (MQ=255)                     aTGCAGTGCATACCGATATCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGCATGCCGCTTGGATGAACTTTg                                                                                                                              <  2:36841/150‑1 (MQ=255)                       gCAGTGCATACCGATATCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGCATGCCGCTTGGCTGAACTTTGTCg                                                                                                                           <  2:200758/151‑1 (MQ=255)                          gTGCATACCGATATCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGCATGCCGCTTGGCTGAACTTTGTCGtt                                                                                                                         <  1:383923/150‑1 (MQ=255)                          gTGCATACCGATATCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGCATGCCGCTTGGCTGAACTTTGTCGtt                                                                                                                         >  2:163697/1‑150 (MQ=255)                            gCATACCGATATCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTTCCGCTCCGGGCGCTCGCCCGCATGCCGCTTGGCTGAACTTTGTCGTTAg                                                                                                                       <  1:8258/150‑1 (MQ=255)                             cATACCGATATCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGCATGCCGCTTGGCTGAACTTTGTCGTTAGCt                                                                                                                     <  2:359609/151‑1 (MQ=255)                              ataccgataccgGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGCATGCCGCTTGGCTGAACTTTGTCGTTAGCTc                                                                                                                    <  2:366562/151‑1 (MQ=255)                              aTACCGATATCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGCATGCCGCTTGGCTGAACTTTGTCGTTAGCTc                                                                                                                    <  2:189775/151‑1 (MQ=255)                                  cGATATCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGCATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGaa                                                                                                                 >  1:281602/1‑150 (MQ=255)                                   gATATCGGTCATGCCTGCGTGGGCGTACGCGTTGACCGCCGGCCTTACCCGCTGTCGCGGCCGCTTACCAGCGGTCACACCGTTGAAATCATTACCGCGCCGGGCGCTCGCCCGCATGCCGCTTGGCTGACCTTTTTCGTTAGCTCGAAAg                                                                                                               <  1:651608/151‑1 (MQ=255)                                        cGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGCATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAgcgcgc                                                                                                          <  2:276023/151‑1 (MQ=255)                                         ggTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGCATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAgcgcgcg                                                                                                         <  1:544200/151‑1 (MQ=255)                                         ggTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGCATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAgcgcgcg                                                                                                         <  1:470539/151‑1 (MQ=255)                                           tCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGCATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGcc                                                                                                       >  2:483378/1‑151 (MQ=255)                                               gCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGCATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCaaaa                                                                                                   <  1:501802/151‑1 (MQ=255)                                               gCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGCATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCaaa                                                                                                    <  2:463546/150‑1 (MQ=255)                                                   gCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGCATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTc                                                                                                <  1:316450/150‑1 (MQ=255)                                                    cGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGCATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCg                                                                                               >  2:315046/1‑150 (MQ=255)                                                     gTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGCATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTc                                                                                             >  2:281010/1‑151 (MQ=255)                                                        ggCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGCATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGt                                                                                          >  2:380510/1‑151 (MQ=255)                                                                      ccGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGCATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTc                                                                            <  2:466410/151‑1 (MQ=255)                                                                        gCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGCATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCaa                                                                          <  2:545215/151‑1 (MQ=255)                                                                            gCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGCATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGt                                                                      <  2:433788/151‑1 (MQ=255)                                                                             ccTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCCCCGGGCGCACGCCCGCATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAACATTCGGCAGTTGCTGAAAAACCTCAAGCGtg                                                                     >  1:217887/1‑151 (MQ=255)                                                                              cTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGCATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGtg                                                                     >  1:311565/1‑150 (MQ=255)                                                                                        gTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGCATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGt                                                           >  1:325956/1‑150 (MQ=255)                                                                                        gTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGCATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGt                                                           <  2:259270/150‑1 (MQ=255)                                                                                        gTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGCATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTa                                                          <  2:646675/151‑1 (MQ=255)                                                                                                      ccAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGCATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTGGGCcgtcg                                            >  1:410904/1‑151 (MQ=255)                                                                                                       cAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGCATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTGGGCcgtcgt                                           <  2:296747/151‑1 (MQ=255)                                                                                                       cAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGCATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAAGTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTGGGCcgtcgt                                           <  1:570866/151‑1 (MQ=255)                                                                                                         gCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGCATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTGGGCCGTCGTCt                                         <  2:33035/151‑1 (MQ=255)                                                                                                         gCGGACAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGCATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGAGATGATTCTGTAAGTCTGGGCCGCCGTCt                                         >  1:620030/1‑151 (MQ=255)                                                                                                          cGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGCATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCACAATTCGTCAGTTGCTGAAAAACCTCACGCGTGATGATTCTGTAAGCCTGGGCCGTCGTCTg                                        >  1:237863/1‑151 (MQ=255)                                                                                                                   cGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGCATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTGGGCCGTCGTCTGCTCAACCAt                               <  2:163295/151‑1 (MQ=255)                                                                                                                          aTCATTACCGCTCCGGGCGCTCGCCCGCATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTGGGCCGTCGTCTGCTCAACCATGCTTTgg                        <  2:462184/151‑1 (MQ=255)                                                                                                                           tCATTACCGCTCCGGGCGCTCGCCCGCATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTGGGCCGTCGTCTGCTCAACCATGCTTTgg                        <  1:461109/150‑1 (MQ=255)                                                                                                                                aCCGCTCCGGGCGCTCGCCCGCATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTGGGCCGTCGTCTGCTCAACCATGCTTTGggtggt                   <  1:356032/150‑1 (MQ=255)                                                                                                                                 ccGCTCCGGGCGCTCGCCCGCATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTGGGCCGTCGTCTGCTCAACCATGCTTTGGGTGGTAg                 <  1:638711/151‑1 (MQ=255)                                                                                                                                   gCTCCGGGCGCTCGCCCGCATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTGGGCCGTCGTCTGCTCAACCATGCTTTGGGTGGTAGcc               <  2:332908/151‑1 (MQ=255)                                                                                                                                       cGGGCGCGCGCCCGCATGCCGCTTGGCTGAACTTTGTCGTTATCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTGGGCCGTCGTCTGCTCAACCATGCTTggggag                     <  1:207360/141‑3 (MQ=255)                                                                                                                                            gcTCGCCCGCATGCCGCTTCGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTGGGCCGTCGTCTGCTCAACCATGCTTTGGGTGGTAGCCGTAAGCtg       >  1:294872/1‑150 (MQ=255)                                                                                                                                               cGCCCGCATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTGGGCCGTCGTCTGCTCAACCATGCTTTGGGTGGTAGCCGTAAGCtgaatg   >  1:406201/1‑151 (MQ=255)                                                                                                                                                gCCCGCATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTGGGCCGTCGTCTGCTCAACCATGCTTTGGGTGGTAGCCGTAAGCtgaatga  <  2:311719/151‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                                  AACGCCCGTCGACTTCGCTTATGCAGTGCATACCGATATCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTGGGCCGTCGTCTGCTCAACCATGCTTTGGGTGGTAGCCGTAAGCTGAATGA  >  NC_000913/3823611‑3823904

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑