Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,823,751	C→A	A451D (GCT→GAT)	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	3,823,751	0	C	A	100.0%	204.5 / NA	52	A451D (GCT→GAT)	spoT	bifunctional (p)ppGpp synthetase II/ guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (26/26);  total (26/26)

TGCAACGCCCGTCGACTTCGCTTATGCAGTGCATACCGATATCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTGGGCCGTCGTCTGCTCAACCATGCTTTGGGTGGTAGCCGTAAGCT  >  NC_000913/3823608‑3823898                                                                                                                                                |                                                                                                                                                    tGCAACGCCCGTCGACTTCGCTTATGCAGTGCATACCGATATCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCg                                                                                                                                              >  1:730611/1‑151 (MQ=255)  gCAACGCCCGTCGACTTCGCTTATGCAGTGCATACCGATATCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCCGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCg                                                                                                                                              >  2:185809/1‑150 (MQ=255)    aaCGCCCGTCGACTTCGCTTATGCAGTGCATACCGATATCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAAt                                                                                                                                           >  2:734837/1‑151 (MQ=255)     aCGCCCGTCGACTTCGCTTATGCAGTGCATACCGATATCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATg                                                                                                                                          <  2:273227/151‑1 (MQ=255)        cccGTCGACTTCGCTTATGCAGTGCATACCGATATCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCg                                                                                                                                       >  1:26039/1‑151 (MQ=255)        cccGTCGACTTCGCTTATGCAGTGCATACCGATATCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCg                                                                                                                                       <  1:89891/151‑1 (MQ=255)            tCGACTTCGCTTATGCAGTGCATACCGATATCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTg                                                                                                                                   >  1:459443/1‑151 (MQ=255)               aCTTCGCTTATGCAGTGCATACCGATATCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCt                                                                                                                                <  1:622508/151‑1 (MQ=255)                cTTCGCTTATGCAGTGCATACCGATATCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTg                                                                                                                               >  2:1114/1‑151 (MQ=255)                 ttCGCTTATGCAGTGCATACCGATATCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCCTTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTg                                                                                                                               >  1:76891/1‑150 (MQ=255)                  tCGCTTATGCAGTGCATACCGATATCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGa                                                                                                                              <  1:36382/150‑1 (MQ=255)                       tATGCAGTGCATACCGATATCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACttt                                                                                                                         <  1:499793/150‑1 (MQ=255)                            aGTGCATACCGATATCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGtt                                                                                                                   >  2:387385/1‑151 (MQ=255)                             gTGCATACCGATATCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTa                                                                                                                  <  2:487040/151‑1 (MQ=255)                                cATACCGATATCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCt                                                                                                               >  1:35439/1‑151 (MQ=255)                                cATACCGATATCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCt                                                                                                               >  2:3457/1‑151 (MQ=255)                                cATACCGATATCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCt                                                                                                               >  1:328316/1‑151 (MQ=255)                                    ccGATATCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGa                                                                                                            <  2:413274/150‑1 (MQ=255)                                    ccGATATCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGa                                                                                                            <  2:327410/150‑1 (MQ=255)                                         atCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAgcgc                                                                                                      >  1:507138/1‑151 (MQ=255)                                                      gCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCg                                                                                         >  1:624886/1‑151 (MQ=255)                                                        gTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTc                                                                                       <  1:94416/151‑1 (MQ=255)                                                          gggCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAg                                                                                     <  1:289554/151‑1 (MQ=255)                                                            gcgcACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCAATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGtt                                                                                   >  2:452948/1‑151 (MQ=255)                                                                 cgcgTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGa                                                                              <  2:127856/151‑1 (MQ=255)                                                                         ccGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTc                                                                      <  2:565964/151‑1 (MQ=255)                                                                           gCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCaa                                                                    <  2:391936/151‑1 (MQ=255)                                                                            ccAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCaa                                                                    <  2:162526/150‑1 (MQ=255)                                                                               gCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCg                                                                 >  1:592600/1‑150 (MQ=255)                                                                                    aCCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGtgatga                                                           <  1:357727/151‑1 (MQ=255)                                                                                    aCCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGtgatg                                                            <  2:665255/150‑1 (MQ=255)                                                                                      ccGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGAtt                                                         <  1:625421/151‑1 (MQ=255)                                                                                             cGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTaa                                                   <  1:350275/150‑1 (MQ=255)                                                                                              gCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGc                                                 >  1:431908/1‑151 (MQ=255)                                                                                                aGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCt                                               >  1:569298/1‑151 (MQ=255)                                                                                                    gCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTGGGc                                           >  1:232427/1‑151 (MQ=255)                                                                                                        aCCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTCAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTGGGCcgtc                                       >  2:280189/1‑151 (MQ=255)                                                                                                           aGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTGGGCCgtcgtc                                    >  1:321229/1‑151 (MQ=255)                                                                                                            gCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTGGGCCGTCGTCt                                   >  2:186073/1‑151 (MQ=255)                                                                                                             cGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTGGGCCGTCGTCTg                                  >  1:20914/1‑151 (MQ=255)                                                                                                                  aaaCCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTGGGCCGTCGTCTGCTCaa                             <  1:85327/151‑1 (MQ=255)                                                                                                                  aaaCCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTGGGCCGTCGTCTGCTCa                              >  2:711762/1‑150 (MQ=255)                                                                                                                   aaCCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTGGGCCGTCGTCTGCTCAAc                            <  1:46994/151‑1 (MQ=255)                                                                                                                   aaCCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTGGGCCGTCGTCTGCTCAAc                            >  1:381111/1‑151 (MQ=255)                                                                                                                    aCCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTGGGCCGTCGTCTGCTCAAcc                           <  1:769022/151‑1 (MQ=255)                                                                                                                       gTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTGGGCCGTCGTCTGCTCAACCATg                        <  1:723133/151‑1 (MQ=255)                                                                                                                            aaTCATTACCGATCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAAATCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGACTGGGCCGTCGTATGCTCAACCATGCTTTg                   <  2:269760/151‑1 (MQ=255)                                                                                                                               cATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTGGGCCGTCGTCTGCTCAACCATGCTTTGggt                <  1:394207/151‑1 (MQ=255)                                                                                                                                   aCCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTGGGCCGTCGTCTGCTCAACCATGCTTTGggtggt             >  2:274635/1‑150 (MQ=255)                                                                                                                                    ccGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTGGGCCGTCGTCTGCTCAACCATGCTTTGggtggt             >  1:383962/1‑149 (MQ=255)                                                                                                                                      gCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATGCTGTAAGCCTGGGCCGTCGTCTGCTCAACCATGCTTTGGGTGGTAGcc         <  2:76877/151‑1 (MQ=255)                                                                                                                                         ccGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTGGGCCGTCGTCTGCTCAACCATGCTTTGGGTGGTAGCCg        <  1:185849/149‑1 (MQ=255)                                                                                                                                             gcgaTCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTGGGCCGTCGTCTGCTCAACCATGCTTTGGGTGGTAGCCGTAAGCt  >  2:376315/1‑151 (MQ=255)                                                                                                                                                |                                                                                                                                                    TGCAACGCCCGTCGACTTCGCTTATGCAGTGCATACCGATATCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTGGGCCGTCGTCTGCTCAACCATGCTTTGGGTGGTAGCCGTAAGCT  >  NC_000913/3823608‑3823898

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑