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%	196.4 / NA	50	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 (23/27);  total (23/27)

GTGCGCTGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGAAAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCATG  >  REL606/3762669‑3762811                                                                         |                                                                       gTGCGCTGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGa                                                                     <  1:288203/76‑1 (MQ=255)  tGCGCTGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGagatagat                                                                    >  2:737164/1‑76 (MQ=255)   gcgcTGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATg                                                                   <  1:1669122/76‑1 (MQ=255)   gcgcTGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATg                                                                   >  1:1709475/1‑76 (MQ=255)       tGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTcg                                                               >  1:517800/1‑76 (MQ=255)       tGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTcg                                                               <  1:1254028/76‑1 (MQ=255)       tGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTcg                                                               <  2:134257/76‑1 (MQ=255)        ggCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTcgc                                                              >  2:1590466/1‑76 (MQ=255)             aCCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTa                                                         <  1:1207015/76‑1 (MQ=255)             aCCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTa                                                         <  1:306882/76‑1 (MQ=255)              ccTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTAc                                                        >  1:1469286/1‑76 (MQ=255)              ccTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTAc                                                        <  1:9133/76‑1 (MQ=255)               cTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACa                                                       >  2:739610/1‑76 (MQ=255)                tGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAg                                                      <  2:1437087/76‑1 (MQ=255)                      cggcAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACAGAAGAGATAGATGGTCGCGTCTACAGCGCCtt                                                >  2:1670119/1‑76 (MQ=255)                          aaTTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAATAGATAGATGGTCGCGTCTACAGCGCCTTTAtt                                            <  2:1621832/76‑1 (MQ=255)                          aaTTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTAtt                                            <  1:999428/76‑1 (MQ=255)                           aTTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTc                                           >  1:367085/1‑76 (MQ=255)                            ttAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCg                                          >  1:1501688/1‑76 (MQ=255)                                caccacGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTg                                      <  1:2029491/76‑1 (MQ=255)                                 accacGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGa                                     <  1:2050488/76‑1 (MQ=255)                                   cacGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGAcc                                   <  2:581031/76‑1 (MQ=255)                                      gACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCt                                <  2:41501/76‑1 (MQ=255)                                       aCTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTc                               <  1:17731/76‑1 (MQ=255)                                         ttCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGt                             <  1:1040000/76‑1 (MQ=255)                                          tCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTg                            <  1:67873/76‑1 (MQ=255)                                           cGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGa                           >  1:1059409/1‑76 (MQ=255)                                           cGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGa                           >  1:136015/1‑76 (MQ=255)                                            gAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGAc                          >  1:1962525/1‑76 (MQ=255)                                              atatTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCg                        >  2:1358406/1‑76 (MQ=255)                                               tatTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCgt                       >  2:586129/1‑76 (MQ=255)                                               tatTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCgt                       >  1:2060646/1‑76 (MQ=255)                                                 ttCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCgtgt                     >  1:611166/1‑76 (MQ=255)                                                  tCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGtgtg                    <  2:776698/76‑1 (MQ=255)                                                    aaaGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCa                  <  2:1331114/76‑1 (MQ=255)                                                     aaGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCAt                 >  1:1770578/1‑76 (MQ=255)                                                       gTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCt               <  1:23497/76‑1 (MQ=255)                                                       gTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCt               >  1:499201/1‑76 (MQ=255)                                                        tttGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTg              >  2:133236/1‑76 (MQ=255)                                                         ttGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTgg             >  1:594749/1‑76 (MQ=255)                                                         ttGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTgg             >  1:790316/1‑76 (MQ=255)                                                           gAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCg           <  2:594749/76‑1 (MQ=255)                                                           gAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCg           <  1:333382/76‑1 (MQ=255)                                                            aaTACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGa          <  2:951539/76‑1 (MQ=255)                                                            aaTACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGa          <  2:1528591/76‑1 (MQ=255)                                                             aTACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGaa         >  1:810573/1‑76 (MQ=255)                                                              tACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAat        <  1:86241/76‑1 (MQ=255)                                                               aCGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAata       <  1:655983/76‑1 (MQ=255)                                                                cGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAatat      >  1:206671/1‑76 (MQ=255)                                                                   aaGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCAt   <  2:1835141/76‑1 (MQ=255)                                                                    agagATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCATg  >  1:787956/1‑76 (MQ=255)                                                                         |                                                                       GTGCGCTGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGAAAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCATG  >  REL606/3762669‑3762811

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑