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%	193.6 / NA	51	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 (21/30);  total (21/30)

GTGCAACGCCCGTCGACTTCGCTTATGCAGTGCATACCGATATCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTGGGCCGTCGTCTGCTCAACCATGCTTTGGGTGGTAGCCGTA  >  NC_000913/3823607‑3823894                                                                                                                                                 |                                                                                                                                                gTGCAACGCCCGTCGACTTCGCTTATGCAGTGCATACCGATATCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGccc                                                                                                                                           >  2:670993/1‑151 (MQ=255)  tGCAACGCCCGTCGACTTCGCTTATGCAGTGCATACCGATATCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCg                                                                                                                                          >  1:660972/1‑151 (MQ=255)      aCGCCCGTCGACTTCGCTTATGCAGTGCATACCGATATCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATg                                                                                                                                      <  1:148653/151‑1 (MQ=255)         cccGTCGACTTCGCTTATGCAGTGCATACCGATATCGGTCATGCCTGCGTGGGCGCCCGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATg                                                                                                                                      <  2:411034/148‑1 (MQ=255)          ccGTCGACTTCGCTTATGCAGTGCATACCGATATCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGc                                                                                                                                  >  2:84576/1‑151 (MQ=255)            gTCGACTTCGCTTATGCAGTGCATACCGATATCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCtt                                                                                                                                <  1:402069/151‑1 (MQ=255)            gTCGACTTCGCTTATGCAGTGCATACCGATATCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCtt                                                                                                                                <  2:177677/151‑1 (MQ=255)             tCGACTTCGCTTATGCAGTGCATACCGATATCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTg                                                                                                                               >  2:579233/1‑151 (MQ=255)               gACTTCGCTTATGCAGTGCATACCGATATCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCt                                                                                                                                 <  2:249006/147‑1 (MQ=255)               gACTTCGCTTATGCAGTGCATACCGATATCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGc                                                                                                                             <  1:640369/151‑1 (MQ=255)               gACTTCGCTTATGCAGTGCATACCGATATCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAACGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGc                                                                                                                             >  2:172991/1‑151 (MQ=255)                aCTTCGCTTATGCAGTGCATACCGATATCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTg                                                                                                                               >  2:392923/1‑148 (MQ=255)                     gCTTATGCAGTGCATACCGATATCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACt                                                                                                                       <  1:25855/151‑1 (MQ=255)                       ttATGCAGTGCATACCGATATCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACttt                                                                                                                     >  2:634377/1‑151 (MQ=255)                        tATGCAGTGCATACCGATATCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGCCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACttt                                                                                                                     >  2:78796/1‑150 (MQ=255)                         aggCAGTGCATACCGATATCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACtt                                                                                                                      <  2:223279/146‑1 (MQ=255)                         aTGCAGTGCATACCGATATCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAAGCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACttt                                                                                                                     <  2:442069/149‑1 (MQ=255)                           gCAGTGCATACCGATATCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCg                                                                                                                 <  2:363958/151‑1 (MQ=255)                             aGTGCATACCGATATCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGtt                                                                                                               <  2:401245/151‑1 (MQ=255)                                         tatCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAgcg                                                                                                   >  1:535881/1‑151 (MQ=255)                                             ggTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAgcgcgcg                                                                                               >  1:121742/1‑151 (MQ=255)                                                cATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGcc                                                                                             >  1:425689/1‑150 (MQ=255)                                                cATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCa                                                                                            <  2:598169/151‑1 (MQ=255)                                                   gCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCaaa                                                                                          <  1:176148/150‑1 (MQ=255)                                                       gCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCg                                                                                     <  1:610380/151‑1 (MQ=255)                                                           gggCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCCGCTGTCCGGCCGTTGCTTTCCTTACCGATAGTGGCGATTGATCTGTTTTCTTTTGGCTGAAATTTGTCGTTAGCTCGCTCTCGCGCGCCatcgttagtga                                                                                  <  2:7912/150‑11 (MQ=255)                                                                          ccGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCt                                                                   <  2:362066/150‑1 (MQ=255)                                                                          ccGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTc                                                                  <  2:57124/151‑1 (MQ=255)                                                                             ccAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAg                                                               <  1:614890/151‑1 (MQ=255)                                                                               aGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCg                                                             <  1:85076/151‑1 (MQ=255)                                                                                    tACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGtgat                                                         <  2:194347/150‑1 (MQ=255)                                                                                     aCCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGtgatg                                                        >  1:645285/1‑150 (MQ=255)                                                                                       ccGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGAtt                                                     >  2:429754/1‑151 (MQ=255)                                                                                         gCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCt                                                   <  2:65509/151‑1 (MQ=255)                                                                                              cGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAg                                              <  1:331672/151‑1 (MQ=255)                                                                                                   ccGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTgg                                         <  1:182109/151‑1 (MQ=255)                                                                                                       ttACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTGGGCcg                                     >  1:17053/1‑151 (MQ=255)                                                                                                        tACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTGGGCcg                                     <  2:677928/150‑1 (MQ=255)                                                                                                         aCCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTGGGCcgtc                                   <  2:230032/151‑1 (MQ=255)                                                                                                            aGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTGGGCCgtcgtc                                >  2:539239/1‑151 (MQ=255)                                                                                                               ggTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTGGGCCGTCGTCTGc                             >  1:666540/1‑151 (MQ=255)                                                                                                                gTCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTGGGCCGTCGTCTGCt                            >  1:284447/1‑151 (MQ=255)                                                                                                                 tCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTGGGCCGTCGTCTGCTc                           >  2:686369/1‑151 (MQ=255)                                                                                                                 tCAAACCGTTGAAATCATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTGGGCCGTCGTCTGCTc                           >  2:634372/1‑151 (MQ=255)                                                                                                                                cATTACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTGGGCCGTCGTCTGCTCAACCATGCTTTGggt            <  1:255678/151‑1 (MQ=255)                                                                                                                                cATTACCGCTCCGGGCGATCGCCAGAATGCCGCTTGGCTGAACTTAGTCGATAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTGGGCCGTCGTCTGCTCAACCATGCTTTGggt            >  2:104417/1‑151 (MQ=255)                                                                                                                                  ttACCGCTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTGGGCCGTCGTCTGCTCAACCATGCTTTGggtgg          >  1:226250/1‑151 (MQ=255)                                                                                                                                        cTCCGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTGGGCCGTCGTCTGCTCAACCATGCTTTGGGTGGTAGcc     <  2:22956/150‑1 (MQ=255)                                                                                                                                          ccGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTGGGCCGTCGTCTGCTCAACCATGCTTTGGGTGGTAGCCg    <  2:355750/149‑1 (MQ=255)                                                                                                                                          ccGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTGGGCCGTCGTCTGCTCAACCATGCTTTGGGTGGTAGCCGt   <  1:58589/150‑1 (MQ=255)                                                                                                                                          ccGGGCGATCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTGGGCCGTCGTCTGCTCAACCATGCTTTGGGTGGTAGCCGTa  <  2:425542/151‑1 (MQ=255)                                                                                                                                                 |                                                                                                                                                GTGCAACGCCCGTCGACTTCGCTTATGCAGTGCATACCGATATCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTGGGCCGTCGTCTGCTCAACCATGCTTTGGGTGGTAGCCGTA  >  NC_000913/3823607‑3823894

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑