Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	REL606	3,762,741	A→T	K662I (AAA→ATA)	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
*	REL606	3,762,741	0	A	T	100.0%	144.0 / NA	37	K662I (AAA→ATA)	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 T (20/17);  total (20/17)

GTGCGCTGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGAAAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCATG  >  REL606/3762669‑3762811                                                                         |                                                                       gTGCGCTGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGa                                                                     <  1:1339/76‑1 (MQ=255)  tGCGCTGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGagatagat                                                                    <  1:612572/76‑1 (MQ=255)   gcgcTGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATg                                                                   <  1:215011/76‑1 (MQ=255)   gcgcTGGCAAACCCGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATg                                                                   >  1:81435/1‑76 (MQ=255)       tGGCAAACCTGACGGCGGNAATTAACACCACGACTTCGAGTATTCATAGTTTGAATACGGAAGAGATAGATGGTcg                                                               >  1:1114827/1‑76 (MQ=255)       tGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATTGTcg                                                               <  1:338053/76‑1 (MQ=255)       tGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTcg                                                               <  1:983315/76‑1 (MQ=255)       tGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTcg                                                               >  1:566868/1‑76 (MQ=255)         gCAAACCTGACGGCGGCAAGTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTcgcg                                                             <  1:895848/76‑1 (MQ=255)          cAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGt                                                            >  1:753374/1‑76 (MQ=255)              ccTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTAc                                                        >  2:628469/1‑76 (MQ=255)                tGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAg                                                      >  2:361620/1‑76 (MQ=255)                  aCGGCGGCAATTAAGACCACGACTTCGATTANTCAAAGTTTGAATANGGAAGNGATAGATGGTCGCTTCTACAgcg                                                    <  2:152556/76‑1 (MQ=255)                      cggcAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCtt                                                <  1:202544/76‑1 (MQ=255)                         cAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTAt                                             >  1:90245/1‑76 (MQ=255)                              aaCACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTc                                        >  2:444008/1‑76 (MQ=255)                                 accacGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGa                                     >  1:931544/1‑76 (MQ=255)                                   cacGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGAcc                                   >  1:895657/1‑76 (MQ=255)                                     cGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGc                                 >  2:464959/1‑76 (MQ=255)                                         ttCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGt                             <  2:269301/76‑1 (MQ=255)                                           cGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGa                           >  1:1031029/1‑76 (MQ=255)                                            gAATATGCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTAGAGCGCCTTTATTCGTCTGACCGCTCGTGAc                          <  1:1067629/76‑1 (MQ=255)                                               tatTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACATCGCCTTTATTCGTCTGACCGCTCGTGACCgt                       >  2:186639/1‑76 (MQ=255)                                                atTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCgtg                      <  1:1071744/76‑1 (MQ=255)                                                  tCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGtgtg                    <  1:108976/76‑1 (MQ=255)                                                        tttGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTg              >  1:861291/1‑76 (MQ=255)                                                         ttGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTgg             <  1:841625/76‑1 (MQ=255)                                                          tGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGc            <  1:1140186/76‑1 (MQ=255)                                                          tGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGc            >  2:651401/1‑76 (MQ=255)                                                           gAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCg           <  1:626984/76‑1 (MQ=255)                                                           gAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCg           >  1:160341/1‑76 (MQ=255)                                                            aaTACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGa          >  2:663142/1‑76 (MQ=255)                                                               aCGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAata       <  1:511447/76‑1 (MQ=255)                                                               aCGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAata       <  1:156957/76‑1 (MQ=255)                                                                 ggAAGAGATAGATGGTCGCGTCTGCAGCGCCTTTATTCGTCTGACCCCTCGTGACCGCGTGCATCTGGAGAATATc     >  1:56944/1‑76 (MQ=255)                                                                 ggAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATc     >  2:855289/1‑76 (MQ=255)                                                                   aaGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCAt   >  2:937673/1‑76 (MQ=255)                                                                    agagATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCATg  <  2:359998/76‑1 (MQ=255)                                                                         |                                                                       GTGCGCTGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGAAAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCATG  >  REL606/3762669‑3762811

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑