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%	208.3 / NA	54	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 (24/30);  total (24/30)

TGCGCTGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGAAAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCATGC  >  REL606/3762670‑3762812                                                                        |                                                                        tGCGCTGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTGAAAGTTTGAATACGGAAGagatagat                                                                     <  1:1541494/76‑1 (MQ=255)   cgcTGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATgg                                                                   <  2:489645/76‑1 (MQ=255)         cAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGt                                                             <  2:814317/76‑1 (MQ=255)         cAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGt                                                             <  2:402435/76‑1 (MQ=255)         cAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGt                                                             <  2:814307/76‑1 (MQ=255)           aaCCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCt                                                           >  2:590908/1‑76 (MQ=255)            aCCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTa                                                          <  1:1297837/76‑1 (MQ=255)             ccTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTAc                                                         <  1:240219/76‑1 (MQ=255)               tGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAg                                                       <  1:872155/76‑1 (MQ=255)               tGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAg                                                       >  2:120484/1‑76 (MQ=255)               tGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAg                                                       >  2:1256633/1‑76 (MQ=255)               tGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAg                                                       <  2:1448479/76‑1 (MQ=255)               tGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAg                                                       <  2:347792/76‑1 (MQ=255)               tGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAg                                                       >  1:109746/1‑76 (MQ=255)                 aCGGCGGCAATTAACACCACGACTTCGAAGATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAgcg                                                     <  2:311179/76‑1 (MQ=255)                      ggcAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCttt                                                >  1:1011858/1‑76 (MQ=255)                       gcAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTa                                               <  2:550504/76‑1 (MQ=255)                         aaTTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTAtt                                             <  2:212624/76‑1 (MQ=255)                         aaTTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTAtt                                             <  1:1598676/76‑1 (MQ=255)                         aaTTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTAtt                                             >  2:1105591/1‑76 (MQ=255)                         aaTTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGAGGGTCGCGTCTACAGCGCCTTTAtt                                             <  2:614449/76‑1 (MQ=255)                         aaTTAACACCACGACTTCGAATATTCAAAGTTTGAATACGCAAGAGATAGATGGTCGCGTCTACAGCCCCTTTAtt                                             >  2:1105606/1‑76 (MQ=255)                          aTTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTc                                            >  1:642253/1‑76 (MQ=255)                          aTTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTc                                            >  2:721231/1‑76 (MQ=255)                             aaCACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTc                                         >  1:770839/1‑76 (MQ=255)                               caccacGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTg                                       >  1:1664828/1‑76 (MQ=255)                                accacGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGa                                      <  1:1787755/76‑1 (MQ=255)                                accacGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGa                                      <  1:657109/76‑1 (MQ=255)                                accacGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGa                                      <  2:589527/76‑1 (MQ=255)                                      aCTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTc                                <  1:819138/76‑1 (MQ=255)                                       cTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCg                               <  1:1555094/76‑1 (MQ=255)                                         tCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTg                             <  1:422062/76‑1 (MQ=255)                                          cGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGa                            >  1:1405177/1‑76 (MQ=255)                                            aaTATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCATTTATTCGTCTGACCGCTCGTGAcc                          >  2:569974/1‑76 (MQ=255)                                             atatTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCg                         >  2:1484684/1‑76 (MQ=255)                                               atTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCgtg                       <  2:1830777/76‑1 (MQ=255)                                                  cAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGc                    <  2:420596/76‑1 (MQ=255)                                                   aaaGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCa                   <  2:1662806/76‑1 (MQ=255)                                                   aaaGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCa                   <  1:210221/76‑1 (MQ=255)                                                    aaGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCAt                  >  2:557860/1‑76 (MQ=255)                                                    aaGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCAt                  >  1:1028855/1‑76 (MQ=255)                                                       tttGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTg               >  1:728364/1‑76 (MQ=255)                                                         tGAATACGGAAG‑GGTAGATGGTCGCGGCTACAGGCCCTTTAATCGTCTGACCGCTCGTGACCGTGGGCATTTTGCg            >  2:148731/1‑76 (MQ=255)                                                          gAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCg            <  2:1838272/76‑1 (MQ=255)                                                          gAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCg            <  2:386610/76‑1 (MQ=255)                                                          gAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCg            <  2:754318/76‑1 (MQ=255)                                                            aTACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCCTCTGGCGaa          >  2:1140218/1‑76 (MQ=255)                                                            aTACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGaa          >  2:233305/1‑76 (MQ=255)                                                            aTACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGaa          >  1:1790567/1‑76 (MQ=255)                                                               cgaaaGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAatat       <  1:754550/73‑1 (MQ=255)                                                               cGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAatat       <  1:281844/76‑1 (MQ=255)                                                                ggAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATc      >  2:731249/1‑76 (MQ=255)                                                                 gAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCa     <  1:40666/76‑1 (MQ=255)                                                                 gAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCa     >  1:501810/1‑76 (MQ=255)                                                                  aaGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCAt    <  1:1746744/76‑1 (MQ=255)                                                                   agagATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCATg   >  1:1860011/1‑76 (MQ=255)                                                                    gagaTAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCATgc  >  1:76173/1‑76 (MQ=255)                                                                        |                                                                        TGCGCTGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGAAAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCATGC  >  REL606/3762670‑3762812

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑