Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,823,770	G→T	W457C (TGG→TGT)	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	3,823,770	0	G	T	100.0%	194.1 / NA	53	W457C (TGG→TGT)	spoT	bifunctional (p)ppGpp synthetase II/ guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base T (27/26);  total (27/26)

CTTCGCTTATGCAGTGCATACCGATATCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTGGGCCGTCGTCTGCTCAACCATGCTTTGGGTGGTAGCCGTAAGCTGAATGA  >  NC_000913/3823623‑3823904                                                                                                                                                    |                                                                                                                                       cTTCGCTTATGCAGTGCATACCGATATCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGAATGCCGCTTGTCTg                                                                                                                                     >  1:343319/1‑151 (MQ=255)  ttCGCTTATGCAGTGCATACCGATATCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGAATGCCGCTTGTCTg                                                                                                                                     >  1:754895/1‑150 (MQ=255)   tCGCTTATGCAGTGCATACCGATATCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGAATGCCGCTTGTCTg                                                                                                                                     <  2:608804/149‑1 (MQ=255)      cTTATGCAGTGCATACCGATATCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGAATGCCGCTTGTCTGAACtt                                                                                                                                >  1:842473/1‑151 (MQ=255)         aTGCAGTGCATACCGATATCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGAATGCCGCTTGTCTGAACttt                                                                                                                               <  2:595867/149‑1 (MQ=255)           gCAGTGCATACCGATATCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGAATGCCGCTTGTCTGAACTTTGTc                                                                                                                            <  1:208837/150‑1 (MQ=255)                gCATACCGATATCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGAATGCCGCTTGTCTGAACTTTGTCGTTAGc                                                                                                                      >  2:449594/1‑151 (MQ=255)                  aTACCGATATCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGAATGCCGCTTGTCTGAACTTTGTCGTTAGCTc                                                                                                                    >  1:243171/1‑151 (MQ=255)                    aCCGATATCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGAATGCCGCTTGTCTGAACTTTGTCGTTAGCTCg                                                                                                                   >  1:379818/1‑150 (MQ=255)                          atCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGAATGCCGCTTGTCTGAACTTTGTCGTTAGCTCGAAAgcgc                                                                                                            >  2:624242/1‑151 (MQ=255)                          atCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGAATGCCGCTTGTCTGAACTTTGTCGTTAGCTCGAAAgcgc                                                                                                            <  1:482169/151‑1 (MQ=255)                          atCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGAATGCCGCTTGTCTGAACTTTGTCGTTAGCTCGAAAgcgc                                                                                                            <  1:636398/151‑1 (MQ=255)                          atCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGAATGCCGCTTGTCTGAACTTTGTCGTTAGCTCGAAAgcgc                                                                                                            <  1:678426/151‑1 (MQ=255)                          atCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGAATGCCGCTTGTCTGAACTTTGTCGTTAGCTCGAAAgcgc                                                                                                            <  2:655839/151‑1 (MQ=255)                            cGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGAATGCCGCTTGTCTGAACTTTGTCGTTAGCTCGAAAgcgcgc                                                                                                          <  1:401376/151‑1 (MQ=255)                            cGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGAATGCCGCTTGTCTGAACTTTGTCGTTAGCTCGAAAgcgcgc                                                                                                          >  2:715282/1‑151 (MQ=255)                               tCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGAATGCCGCTTGTCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGcc                                                                                                       >  2:685814/1‑151 (MQ=255)                                cATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGAATGCCGCTTGTCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCa                                                                                                      <  1:10822/151‑1 (MQ=255)                                cATGCCTGCGTGGGCGCACGCGTTGACCACCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGAATGCCGCTTGTCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCa                                                                                                      <  2:79815/151‑1 (MQ=255)                                   gCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGAATGCCGCTTGTCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCaaa                                                                                                    >  2:154714/1‑150 (MQ=255)                                      tGCGTGGGCGCACGCGTTGACCCCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGCAATCATTACCGCTCCGGGCGCTCGCCCGAATGCCGCTTGTCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTc                                                                                                >  2:54373/1‑151 (MQ=255)                                       gCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGAATGCCGCTTGTCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAAtt                                                                                                 <  2:192267/149‑1 (MQ=255)                                       gCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGAATGCCGCTTGTCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTc                                                                                                <  2:811323/150‑1 (MQ=255)                                           gggCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGAATGCCGCTTGTCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTc                                                                                             >  1:731608/1‑149 (MQ=255)                                            ggCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGAATGCCGCTTGTCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGt                                                                                          >  2:364195/1‑151 (MQ=255)                                              cgcACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGAATGCCGCTTGTCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGtt                                                                                         >  2:633357/1‑150 (MQ=255)                                                   gcgTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGAATGCCGCTTGTCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGa                                                                                    <  2:342145/150‑1 (MQ=255)                                                   gcgTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGAATGCCGCTTGTCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAACTCGTCAGTTGCTGaa                                                                                   <  1:248216/151‑1 (MQ=255)                                                     gTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGAATGCCGCTTGTCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGaaa                                                                                  >  1:347223/1‑150 (MQ=255)                                                         aCCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGAATGCCGCTTGTCTGAACTTTGCCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGACAAAcc                                                                              >  2:673383/1‑150 (MQ=255)                                                                   ttACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGAATGCCGCTTGTCTGAACTTTGTCGTTAGCCCGAAAGCGCGCGACAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGtga                                                                    >  2:47920/1‑150 (MQ=255)                                                                    tACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGAATGCCGCTTGTCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGtga                                                                    <  2:147330/149‑1 (MQ=255)                                                                      cccGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGAATGCCGCTTGTCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTgatgat                                                                <  1:785408/151‑1 (MQ=255)                                                                              cGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGAATGCCGCTTGTCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAg                                                        <  2:747942/151‑1 (MQ=255)                                                                                   ccGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGAATGCCGCTTGTCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTgg                                                   <  2:315/151‑1 (MQ=255)                                                                                    cGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGAATGCCGCTTGTCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTggg                                                  <  2:682800/151‑1 (MQ=255)                                                                                         aCCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGAATGCCGCTTGTCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTGGGCcgtc                                             <  1:165932/151‑1 (MQ=255)                                                                                               ggTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGAATGCCGCTTGTCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTGGGCCGTCGTCTGc                                       >  2:773718/1‑151 (MQ=255)                                                                                                gTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGAATGCCGCTTGTCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTGGGCCGTCGTCTGCt                                      >  1:112135/1‑151 (MQ=255)                                                                                                gTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGAATGCCGCTTGTCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTGGGCCGTCGTCTGCt                                      >  1:289395/1‑151 (MQ=255)                                                                                                 tCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGAATGCCGCTTGTCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTGGGCCGTCGTCTGCTc                                     >  1:685566/1‑151 (MQ=255)                                                                                                 tCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGAATGCCGCTTGTCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTGGGCCGTCGTCTGCTc                                     >  2:538286/1‑151 (MQ=255)                                                                                                                 aTTACCGCTCCGGGCGCTCGCCCGAATGCCGCTTGTCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTGGGCCGTCGTCTGCTCAACCATGCTTTGggtg                     >  2:245802/1‑151 (MQ=255)                                                                                                                 aTTACCGCTCCGGGCGCTCGCCCGAATGCCGCTTGTCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTGGGCCGTCGTCTGCTCAACCATGCTTTGggtg                     <  2:67590/151‑1 (MQ=255)                                                                                                                   tACCGCTCCGGGCGCTCGCCCGAATGCCGCTTGTCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTGGGCCGTCGTCTGCTCAACCATGCTTTGggtgg                    <  2:795248/150‑1 (MQ=255)                                                                                                                    aCCGCTCCGGGCGCTCGCCAGAATGCCGCTTGTCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTGGGCCGTCGTCTGCTCAACCATGCTTTGggtggt                   >  2:6930/1‑150 (MQ=255)                                                                                                                        cTCCGGGCGCTCGCCCGAATGCCGCTTGTCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTGGGCCGTCGTCTGCTCAACCATGCTTTGGGTGGTAGcc               <  2:281623/150‑1 (MQ=255)                                                                                                                         tCCGGGCGCTCGCCCGAATGCCGCTTGTCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTGGGCCGTCGTCTGCTCAACCATGCTTTGGGTGGTAGCCGt             >  1:667995/1‑151 (MQ=255)                                                                                                                          ccGGGCGCTCGCCCGAATGCCGCTTGTCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTGGGCCGTCGTCTGCTCAACCATGCTTTGGGTGGTAGCCGt             <  1:273872/150‑1 (MQ=255)                                                                                                                            gggCGCTCGCCCGAATGCCGCTTGTCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTGGGCCGTCGTCTGCTCAACCATGCTTTGGGTGGTAGCCGTa            >  2:672835/1‑149 (MQ=255)                                                                                                                              gcgcTCGCCCGAATGCCGCTTGTCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTGGGCCGTCGTCTGCTCAACCATGCTTTGGGTGGTAGCCGTAAGCt        >  2:532734/1‑151 (MQ=255)                                                                                                                               cgcTCGCCCGAATGCCGCTTGTCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTGGGCCGTCGTCTGCTCAACCATGCTTTGGGTGGTAGCCGTAAGCtg       <  2:452874/151‑1 (MQ=255)                                                                                                                                    gCCCGAATGCCGCTTGTCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTGGGCCGTCGTCTGCTCAACCATGCTTTGGGTGGTAGCCGTAAGCtgaatga  <  2:691642/151‑1 (MQ=255)                                                                                                                                                    |                                                                                                                                       CTTCGCTTATGCAGTGCATACCGATATCGGTCATGCCTGCGTGGGCGCACGCGTTGACCGCCAGCCTTACCCGCTGTCGCAGCCGCTTACCAGCGGTCAAACCGTTGAAATCATTACCGCTCCGGGCGCTCGCCCGAATGCCGCTTGGCTGAACTTTGTCGTTAGCTCGAAAGCGCGCGCCAAAATTCGTCAGTTGCTGAAAAACCTCAAGCGTGATGATTCTGTAAGCCTGGGCCGTCGTCTGCTCAACCATGCTTTGGGTGGTAGCCGTAAGCTGAATGA  >  NC_000913/3823623‑3823904

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑