Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,824,507	A→C	*703S (TAA→TCA)	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	3,824,507	0	A	C	100.0%	217.5 / NA	57	*703S (TAA→TCA)	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 (34/23);  total (34/23)

CAAAGTTTGAATACGGAAGAGAAAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCATGCGCAAAATCCGCGTGATGCCAGACGTGATTAAAGTCACCCGAAACCGAAATTAATGTTTTATGAACCCAACACGTTATGCACGCATCTGCGAAATGCTCGCCAGGCGGCAGCCTGATCTGACCGTCTGCATGGAGCAGGTCCACAAACCTCATAACGTTTCTGCGATTATTCGTACCGCAGATGCCGTTGGCGTACATG  >  NC_000913/3824362‑3824653                                                                                                                                                  |                                                                                                                                                   cAAAGTTTGAATACGGAAGAGAAAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCATGCGCAAAATCCGCGTGATGCCAGACGTGATTAAAGTCACCCGAAACCGAAATTCATGtt                                                                                                                                               <  2:875168/151‑1 (MQ=255)     gTTTGAATACGGAAGAGAAAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCATGCGCAAAATCCGCGTGATGCCAGACGTGATTAAAGTCACCCGAAACCGAAATTCATGTTTTAt                                                                                                                                           >  1:367021/1‑151 (MQ=255)       ttGAATACGGAAGAGAAAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCATGCGCAAAATCCGCGTGATGCCAGACGTGATTAAAGTCACCCGAAACCGAAATTCATGTTTTATg                                                                                                                                          <  1:343327/150‑1 (MQ=255)          aaTACGGAAGAGAAAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCATGCGCAAAATCCGCGTGATGCCAGACGTGATTAAAGTCACCCGAAACCGAAATTCATGTTTTATGAAcc                                                                                                                                      <  1:909882/151‑1 (MQ=255)                gAAGAGAAAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCATGCGCAAAATCCGCGTGATGCCAGACGTGATTAAAGTCACCCGAAACCGAAATTCATGTTTTATGAACCCAacac                                                                                                                                >  2:41482/1‑151 (MQ=255)                gAAGAGAAAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCATGCGCAAAATCCGCGTGATGCCAGACGTGATTAAAGTCACCCGAAACCGAAATTCATGTTTTATGAACCCAacac                                                                                                                                >  2:783594/1‑151 (MQ=255)                gAAGAGAAAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCATGCGCAAAATCCGCGTGATGCCAGACGTGATTAAAGTCACCCGAAACCGAAATTCATGTTTTATGAACCCAacac                                                                                                                                >  1:408439/1‑151 (MQ=255)                 aaGAGAAAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCATGCGCAAAATCCGCGTGATGCCAGACGTGATTAAAGTCACCCGAAACCGAAATTCATGTTTTATGAACCCAACACg                                                                                                                               <  1:176714/151‑1 (MQ=255)                   gagaAAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCATGCGCAAAATCCGCGTGATGCCAGACGTGATTAAAGTCACCCGAAACCGAAATCCATGTTTTATGAACCCAACACGtt                                                                                                                             >  1:211809/1‑151 (MQ=255)                     gaAAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCATGCGCAAAATCCGCGTGATGCCAGACGTGATTAAAGTCACCCGAAACCGAAATTCATGTTTTATGAACCCAACACGTTAt                                                                                                                           <  2:11074/151‑1 (MQ=255)                         gATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCATGCGCAAAATCCGCGTGATGCCAGACGTGATTAAAGTCACCCGAAACCGAAATTCATGTTTTATGAACCCAACACGTTATGCAc                                                                                                                       >  1:659995/1‑151 (MQ=255)                               cgcgTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCATGCGCAAAATCCGCGTGATGCCAGACGTGATTAAAGTCACCCGAAACCGAAATTCATGTTTTATGAACCCAACACGTTATGCACGCATCt                                                                                                                 >  1:162328/1‑151 (MQ=255)                                gcgTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCATGCGCAAAATCCGCGTGATGCCAGACGTGATTAAAGTCACCCGAAACCGAAATTCATGTTTTATGAACCCAACACGTTATGCACGCATCTg                                                                                                                <  2:746990/151‑1 (MQ=255)                                gcgTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCATGCGCAAAATCCGCGTGATGCCAGACGTGATTAAAGTCACCCGAAACCGAAATTCATGTTTTATGAACCCAACACGTTATGCACGCATCTg                                                                                                                >  1:132581/1‑151 (MQ=255)                                  gTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCATGCGCAAAATCCGCGTGATGCCAGACGTGATTAAAGTCACCCGAAACCGAAATTCATGTTTTATGAACCCAACACGTTATGCACGCATCTGCg                                                                                                              >  2:408797/1‑151 (MQ=255)                                       cAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCATGCGCAAAATCCGCGTGATGCCAGACGTGATTAAAGTCACCCGAAACCGAAATTCATGTTTTATGAACCCAACACGTTATGCACGCATCTGCGAAAt                                                                                                          >  2:208361/1‑150 (MQ=255)                                        aGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCATGCGCAAAATCCGCGTGATGCCAGACGTGATTAAAGTCACCCGAAACCGAAATTCATGTTTTATGAACCCAACACGTTATGCACGCATCTGCGAAATGc                                                                                                        >  2:563681/1‑151 (MQ=255)                                           gcCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCATGCGCAAAATCCGCGTGATGCCAGACGTGATTAAAGTCACCCGAAACCGAAATTCATGTTTTATGAACCCAACACGTTATGCACGCATCTGCGAAATGCTCg                                                                                                     <  2:304900/151‑1 (MQ=255)                                                 aTTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCATGCGCAAAATCCGCGTGATGCCAGACGTGATTAAAGTCACCCGAAACCGAAATTCATGTTTTATGAACCCAACACGTTATGCACGCATCTGCGAAATGCTCGCCAggc                                                                                               <  1:66020/151‑1 (MQ=255)                                                  ttCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCATGCGCAAAATCCGCGTGATGCCAGACGTGATTAAAGTCACCCGAAACCGAAATTCATGTTTTATGAACCCAACACGTTATGCACGCATCTGCGAAATGCTCGCCAggcg                                                                                              >  1:558412/1‑151 (MQ=255)                                                         gACCGCTCGTGACCGTGTGCATCTGGCGAATATCATGCGCAAAATCCGCGTGATGCCAGACGTGATTAAAGTCACCCGAAACCGAAATTCATGTTTTATGAACCCAACACGTTATGCACGCATCTGCGAAATGCTCGCCAGGCGGCAGc                                                                                         <  1:742619/149‑1 (MQ=255)                                                            cGCTCGTGACCGTGTGCATCTGGCGAATATCATGCGCAAAATCCGCGTGATGCCAGACGTGATTAAAGTCACCCGAAACCGAAATTCATGTTTTATGAACCCAACACGTTATGCACGCATCTGCGAAATGCTCGCCAGGCGGCAGCCTGAt                                                                                    <  1:571956/151‑1 (MQ=255)                                                            cGCTCGTGACCGTGTGCATCTGGCGAATATCATGCGCAAAATCCGCGTGATGCCAGACGTGATTAAAGTCACCCGAAACCGAAATTCATGTTTTATGAACCCAACACGTTATGCACGCATCTGCGAAATGCTCGCCAGGCGGCAGCCTGAt                                                                                    <  1:910926/151‑1 (MQ=255)                                                             gCTCGTGACCGTGTGCATCTGGCGAATATCATGCGCAAAATCCGCGTGATGCCAGACGTGATTAAAGTCACCCGAAACCGAAATTCATGTTTTATGAACCCAACACGTTATGCACGCATCTGCGAAATGCTCGCCAGGTGGCAGCCTGATc                                                                                   >  1:631926/1‑151 (MQ=255)                                                             gCTCGTGACCGTGTGCATCTGGCGAATATCATGCGCAAAATCCGCGTGATGCCAGACGTGATTAAAGTCACCCGAAACCGAAATTCATGTTTTATGAACCCAACACGTTATGCACGCATCTGCGAAATGCTCGCCAGGCGGCAGCCTGATc                                                                                   >  2:118134/1‑151 (MQ=255)                                                                  tGACCGTGTGCATCTGGCGAATATCATGCGCAAAATCCGCGTGATGCCAGACGTGATTAAAGTCACCCGAAACCGAAATTCATGTTTTATGAACCCAACACGTTATGCACGCATCTGCGAAATGCTCGCCAGGCGGCAGCCTGATCTGAcc                                                                              >  2:157553/1‑151 (MQ=255)                                                                   gACCGTGTGCATCTGGCGAATATCATGCGCAAAATCCGCGTGATGCCAGACGTGATTAAAGTCACCCGAAACCGAAATTCATGTTTTATGAACCCAACACGTTATGCACGCATCTGCGAAATGCTCGCCAGGCGGCAGCCTGATCTGACCg                                                                             <  1:366649/151‑1 (MQ=255)                                                                    aCCGTGTGCATCTGGCGAATATCATGCGCAAAATCCGCGTGATGCCAGACGTGATTAAAGTCACCCGAAACCGAAATTCATGTTTTATGAACCCAACACGTTATGCACGCATCTGCGAAATGCTCGCCAGGCGGCAGCCTGATCTGACCGt                                                                            >  1:635193/1‑151 (MQ=255)                                                                      cGTGTGCATCTGGCGAATATCATGCGCAAAATCCGCGTGATGCCAGACGTGATTAAAGTCACCCGAAACCGAAATTCATGTTTTATGAACCCAACACGTTATGCACGCATCTGCGAAATGCTCGCCAGGCGGCAGCCTGATCTGACCGTCt                                                                          >  2:41928/1‑151 (MQ=255)                                                                           gCATCTGGCGAATATCATGCGCAAAATCCGCTTGATGCCAGACGTGATTAAAGTCACCCGAAACCGAAATTCATGTTTTATGAACCCAACACGTTATGCACGCATCTGCGAAATGCTCGCCAGGCGGCAGCCTGATCTGACCGTCTGCAt                                                                      <  1:68739/150‑1 (MQ=255)                                                                                   cGAATATCATGCGCAAAATCCGCGTGATGCCAGACGTGATTAAAGTCACCCGAAACCGAAATTCATGTTTTATGAACCCAACACGTTATGCACGCATCTGCGAAATGCTCGCCAGGCGGCAGCCTGATCTGACCGTCTGCATGGAGCAGGt                                                             >  1:659328/1‑151 (MQ=255)                                                                                    gAATATCATGCGCAAAATCCGCGTGATGCCAGACGTGATTAAAGTCACCCGAAACCGAAATTCATGTTTTATGAACCCAACACGTTATGCACGCATCTGCGAAATGCTCGCCAGGCGGCAGCCTGATCTGACCGTCTGCATGGAGCAGGTc                                                            >  1:564929/1‑151 (MQ=255)                                                                                     aaTATCATGCGCAAAATCCGCGTGATGCCAGACGTGATTAAAGTCACCCGAAACCGAAATTCATGTTTTATGAACCCAACACGTTATGCACGCATCTGCGAAATGCTCGCCAGGCGGCAGCCTGATCTGACCGTCTGCATGGAGCAGGTcc                                                           <  2:487978/151‑1 (MQ=255)                                                                                      atatCATGCGCAAAATCCGCGTGATGCCAGACGTGATTAAAGTCACCCGAAACCGAAATTCATGTTTTATGAACCCAACACGTTATGCACGCATCTGCGAAATGCTCGCCAGGCGGCAGCCTGATCTGACCGTCTGCATGGAGCAGGTcc                                                           >  1:112678/1‑150 (MQ=255)                                                                                          cATGCGCAAAATCCGCGTGATGCCAGACGTGATTAAAGTCACCCGAAACCGAAATTCATGTTTTATGAACCCAACACGTTATGCACGCATCTGCGAAATGCTCGCCAGGCGGCAGCCTGATCTGACCGTCTGCATGGAGCAGGTCCACaa                                                       >  2:520520/1‑150 (MQ=255)                                                                                                cAAAATCCGCGTGATGCCAGACGTGATTAAAGTCACCCGAAACCGAAATTCATGTTTTATGAACCCAACACGTTATGCACGCATCTGCGAAATGCTCGCCAGGCGGCAGCCTGATCTGACCGTCTGCATGGAGCAGGTCCACAAACCTCAt                                                >  1:85903/1‑151 (MQ=255)                                                                                                cAAAATCCGCGTGATGCCAGACGTGATTAAAGTCACCCGAAACCGAAATTCATGTTTTATGAACCCAACACGTTATGCACGCATCTGCGAAATGCTCGCCAGGCGGCAGCCTGATCTGACCGTCTGCATGGAGCAGGTCCACAAACCTCAt                                                <  1:547637/151‑1 (MQ=255)                                                                                                 aaaaTCCGCGTGATGCCAGACGTGATTAAAGTCACCCGAAACCGAAATTCATGTTTTATGAACCCAACACGTTATGCACGCATCTGCGAAATGCTCGCCAGGCGGCAGCCTGATCTGACCGTCTGCATGGAGCAGGTCCACAAACCTCATa                                               <  2:441786/151‑1 (MQ=255)                                                                                                     tCCGCGTGATGCCAGACGTGATTAAAGTCACCCGAAACCGAAATTCATGTTTTATGAACCCAACACGTTATGCACGCATCTGCGAAATGCTCGCCAGGCGGCAGCCTGATCTGACCGTCTGCATGGAGCAGGTCCACAAACCTCATAACGt                                           >  1:902308/1‑151 (MQ=255)                                                                                                     tCCGCGTGATGCCAGACGTGATTAAAGTCACCCGAAACCGAAATTCATGTTTTATGAACCCAACACGTTATGCACGCATCTGCGAAATGCTCGCCAGGCGGCAGCCTGATCTGACCGTCTGCATGGAGCAGGTCCACAAACCTCATAACGt                                           >  1:516774/1‑151 (MQ=255)                                                                                                            gATGCCAGACGTGATTAAAGTCACCCGAAACCGAAATTCATGTTTTATGAACCCAACACGTTATGCACGCATCTGCGAAATGCTCGCCAGGCGGCAGCCTGATCTGACCGTCTGCATGGAGCAGGTCCACAAACCTCATAACGTTTCTGCg                                    >  2:397971/1‑151 (MQ=255)                                                                                                               gCCAGACGTGATTAAAGTCACCCGAAACCGAAATTCATGTTTTATGAACCCAACACGTTATGCACGCATCTGCGAAATGCTCGCCAGGCGGCAGCCTGATCTGACCGTCTGCATGGAGCAGGTCCACAAACCTCATAACGTTTCTGCGatt                                 >  1:568678/1‑151 (MQ=255)                                                                                                               gCCAGACGTGATTAAAGTCACCCGAAACCGAAATTCATGTTTTATGAACCCAACACGTTATGCACGCATCTGCGAAATGCTCGCCAGGCGGCAGCCTGATCTGACCGTCTGCATGGAGCAGGTCCACAAACCTCATAACGTTTCTGCGat                                  <  1:771380/150‑1 (MQ=255)                                                                                                                   gACGTGATTAAAGTCACCCGAAACCGAAATTCATGTTTTATGAACCCAACACGTTATGCACGCATCTGCGAAATGCTCGCCAGGCGGCAGCCTGATCTGACCGTCTGCATGGAGCAGGTCCACAAACCTCATAACGTTTCTGCGATTATTc                             <  1:926989/151‑1 (MQ=255)                                                                                                                      gTGATTAAAGTCACCCGAAACCGAAATTCATGTTTTATGAACCCAACACGTTATGCACGCATCTGCGAAATGCTCGCCAGGCGGCAGCCTGATCTGACCGTCTGCATGGAGCAGGTCCACAAACCTCATAACGTTTCTGCGATTATTCGt                           >  2:121559/1‑150 (MQ=255)                                                                                                                        gATTAAAGTCACCCGAAACCGAAATTCATGTTTTATGAACCCAACACGTTATGCACGCATCTGCGAAATGCTCGCCAGGCGGCAGCCTGATCTGACCGTCTGCATGGAGCAGGTCCACAAACCTCATAACGTTTCTGCGATTATTCGTAcc                        <  2:96883/151‑1 (MQ=255)                                                                                                                         aTTAAAGTCACCCGAAACCGAAATTCATGTTTTATGAACCCAACACGTTATGCACGCATCTGCGAAATGCTCGCCAGGCGGCAGCCTGATCTGACCGTCTGCATGGAGCAGGTCCACAAACCTCATAACGTTTCTGCGATTATTCGTAcct                       <  1:122163/151‑2 (MQ=255)                                                                                                                          ttAAAGTCACCCGAAACCGAAATTCATGTTTTATGAACCCAACACGTTATGCACGCATCTGCGAAATGCTCGCCAGGCGGCAGCCTGATCTGACCGTCTGCATGGAGCAGGTCCACAAACCTCATAACGTTTCTGCGATTATTCGTACCGc                      >  1:827918/1‑151 (MQ=255)                                                                                                                           tAAAGTCACCCGAAACCGAAATTCATGTTTTATGAACCCAACACGTTATGCACGCATCTGCGAAATGCTCGCCAGGCGGCAGCCTGATCTGACCGTCTGCATGGAGCAGGTCCACAAACCTCATAACGTTTCTGCGATTATTCGTACCGc                      >  2:404862/1‑150 (MQ=255)                                                                                                                             aaGTCACCCGAAACCGAAATTCATGTTTTATGAACCCAACACGTTATGCACGCATCTGCGAAATGCTCGCCAGGCGGCAGCCTGATCTGACCGTCTGCATGGAGCAGGTCCACAAACCTCATAACGTTTCTGCGATTATTCGTACCGc                      >  1:850741/1‑148 (MQ=255)                                                                                                                               gTCACCCGAAACCGAAATTCATGTTTTATGAACCCAACACGTTATGCACGCATCTGCGAAATGCTCGCCAGGCGGCAGCCTGATCTGACCGTCTGCATGGAGCAGGTCCACAAACCTCATAACGTTTCTGCGATTATTCGTACCGCAGATg                 <  2:666996/151‑1 (MQ=255)                                                                                                                                 cACCCGAAACCGAAATTCATGTTTTATGAACCCAACACGTTATGCACGCATCTGCGAAATGCTCGCCAGGCGGCAGCCTGATCTGACCGTCTGCATGGAGCAGGTCCACAAACCTCATAACGTTTCTGCGATTATTCGTACCGCAGATGcc               >  1:849892/1‑151 (MQ=255)                                                                                                                                     cgaaaccgaaaTTCATGTTTTATGAACCCAACACGTTATGCACGCATCTGCGAAATGCTCGCCAGGCGGCAGCCTGATCTGACCGTCTGCATGGAGCAGGTCCACAAACCTCATAACGTTTCTGCGATTATTCGTACCGCAGATGCCGTTg           >  1:556849/1‑151 (MQ=255)                                                                                                                                       aaaccgaaaTTCATGTTTTATGAACCCAACACGTTATGCACGCATCTGCGAAATGCTCGCCAGGCGGCAGCCTGATCTGACCGTCTGCATGGAGCAGGTCCACAAACCTCATAACGTTTCTGCGATTATTCGTACCGCAGATGCCGTTGGc         <  2:863447/151‑1 (MQ=255)                                                                                                                                         accgaaaTTCATGTTTTATGAACCCAACACGTTATGCACGCATCTGCGAAATGCTCGCCAGGCGGCAGCCTGATCTGACCGTCTGCATGGAGCAGGTCCACAAACCTCATAACGTTTCTGCGATTATTCGTACCGCAGATGCCGTTGGCGt       >  2:109829/1‑151 (MQ=255)                                                                                                                                              aaTTCATGTTTTATGAACCCAACACGTTATGCACGCATCTGCGAAATGCTCGCCAGGCGGCAGCCTGATCTGACCGTCTGCATGGAGCAGGTCCACAAACCTCATAACGTTTCTGCGATTATTCGTACCGCAGATGCCGTTGGCGTACATg  <  1:408782/151‑1 (MQ=255)                                                                                                                                              aaTTCATGTTTTATGAACCCAACACGTTATGCACGCATCTGCGAAATGCTCGCCAGGCGGCAGCCTGATCTGACCGTCTGCATGGAGCAGGTCCACAAACCTCATAACGTTTCTGCGATTATTCGTACCGCAGATGCCGTTGGCGTACATg  >  1:395840/1‑151 (MQ=255)                                                                                                                                                  |                                                                                                                                                   CAAAGTTTGAATACGGAAGAGAAAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCATGCGCAAAATCCGCGTGATGCCAGACGTGATTAAAGTCACCCGAAACCGAAATTAATGTTTTATGAACCCAACACGTTATGCACGCATCTGCGAAATGCTCGCCAGGCGGCAGCCTGATCTGACCGTCTGCATGGAGCAGGTCCACAAACCTCATAACGTTTCTGCGATTATTCGTACCGCAGATGCCGTTGGCGTACATG  >  NC_000913/3824362‑3824653

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑