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		change	freq	score	reads	annotation	genes	product
*	REL606	3,762,741	0	A→T	100.0%	115.9	39	K662I (AAA→ATA)	spoT	bifunctional (p)ppGpp synthetase II/ guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase
Reads supporting (aligned to +/- strand):  new base (24/14):  ref base (0/0):  total (24/15)

CTTCGAATATTCAAAGTTTGAATACGGAAGAGAAAGATGGTCGCGTCTACAGCGCCTTTATTCGTC  >  REL606/3762708‑3762773                                  |                                 cTTCGAATATTCAAAGTTTGAATACGGAAGAGATAg                                >  1:1541789/1‑36 (MQ=255) cTTCGAATATTCAAAGTTTGAATACGGAAGAGATAg                                >  1:3972528/1‑36 (MQ=255)   tCGAATATTCAAAGTTTGAATACGGAAGAGATAGAt                              <  1:349403/36‑1 (MQ=255)    cGAATATTCAAAGTTTGAATACGGAAGAGATAGATg                             <  1:51621/36‑1 (MQ=255)    cGAATAATCAAAGTTTGAATACGGAAGAGATAGATg                             <  1:1429063/36‑1 (MQ=25)    cGAAGAGTCAGAGTTGGAATACGGAAGAGATAGATg                             <  1:936246/36‑1 (MQ=12)     gAATATTCAAAGTTTGAATACGGAAGAGATAGATgg                            >  1:5552763/1‑36 (MQ=255)     gAATATTCAAAGTTTGAATACGGAAGAGATAGATgg                            >  1:4153005/1‑36 (MQ=255)       atatTCAAAGTTTGAATACGGAAGAGATAGATGGTc                          >  1:2959497/1‑36 (MQ=255)       atatTCAAAGTTTGAATACCGAAGAGATACATggcc                          >  1:242603/1‑34 (MQ=21)          ttCAAAGTTTGAATACGGAACAGGTAGATGGTcggt                       >  1:3955164/1‑34 (MQ=18)            cAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTc                     >  1:6348123/1‑36 (MQ=255)            cAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTc                     <  1:4267979/36‑1 (MQ=255)             aaaGTTTGAATACGGAAGAGATAGATGGTCGCGTCt                    <  1:5122719/36‑1 (MQ=255)               aGTTTGAATACGGAAGAGATAGATGGTCGCGTCTAc                  <  1:2607106/36‑1 (MQ=255)               aGTTTGAATACGGAAGAGATAGATGGTCGCGTCTAc                  <  1:6727264/36‑1 (MQ=255)               aGTTTGAATACGGAAGAGATAGATGGTCGCGTCTAc                  <  1:1407564/36‑1 (MQ=255)               aGTTTGAATACGGAAGAGATAGATGGTCGCCTCTAc                  >  1:6782770/1‑36 (MQ=25)                gTTTGAATACGGAAGAGATAGATGGTCGCGTCTACa                 >  1:5204797/1‑36 (MQ=255)                 tttGAATACGGAAGAGATAGATGGTCGCGTCTACAg                >  1:6331413/1‑36 (MQ=255)                  ttGAATACGGAAGAGATAGATGGTCGCGTCTATAgc               >  1:4283423/1‑36 (MQ=25)                  ttGAATACGGAAGAGATAGATGGTCGCGTCTACAgc               <  1:138356/36‑1 (MQ=255)                   tGAATACGGAAGAGATAGATGGTCGCGTCTACAgcg              >  1:4096224/1‑36 (MQ=255)                   tGAATACGGAAGAGAGAGATGGTCGCGTCTACAgcg              <  1:59172/36‑1 (MQ=255)                    gAATACGGAAGAGATAGATGGTCGCGTCTACAgcgc             <  1:6749681/36‑1 (MQ=255)                     aaTACGGAAGAGATAGATGGTCGCGTCTACAGCGcc            >  1:6813697/1‑36 (MQ=255)                     aaTACGGAAGAGATAGATGGTCGCGTCTACAGCGcc            >  1:6177768/1‑36 (MQ=255)                     aaTACGGAAGAGATAGATGGTCGCGTCTACAGCGcc            >  1:1610083/1‑36 (MQ=255)                     aaTACGGAAGAGATAGATGGTCGCGTCTACAGCGcc            >  1:2199246/1‑36 (MQ=255)                      aTACGGAAGAGATAGATGGTCGCGTCTACAGTGCCt           >  1:4092253/1‑36 (MQ=25)                       tACGGAAGAGATAGATGGTCGCGTCTACAGCGCCtt          >  1:3666513/1‑36 (MQ=255)                        aCGGAAGAGATAGATGGTCGCGTCTACCACGGCttt         >  1:6864686/1‑36 (MQ=18)                          ggAAGAGGTAGATGGTCGCGTCTACAGCGCCTTTAt       <  1:2404201/36‑1 (MQ=25)                          ggAAGAGATAGATGGTCGCGTCTACAGCGCCTTTAt       >  1:4299556/1‑36 (MQ=255)                           gAAGAGATAGATGGGCGCGTCTACAGCGCCTTTAtt      <  1:7460103/36‑1 (MQ=25)                             agagATAGATGGTCGCGTCTACAGCGCCTTTATTCg    >  1:1637628/1‑36 (MQ=255)                             agagATAGATGGTCGCGTCTACAGCGCCTTTATTCg    >  1:3811262/1‑36 (MQ=255)                               agaTAGATGGTCGCGTCTACAGCGCCTTTATTCGTc  <  1:5814254/36‑1 (MQ=255)                               agaTAGATGGTCGCGTCTACAGCGCCTTTATTCGTc  >  1:4969441/1‑36 (MQ=255)                                  |                                 CTTCGAATATTCAAAGTTTGAATACGGAAGAGAAAGATGGTCGCGTCTACAGCGCCTTTATTCGTC  >  REL606/3762708‑3762773 Base quality scores:  ATCG  < 3 ≤  ATCG  < 8 ≤  ATCG  < 17 ≤  ATCG  < 29 ≤  ATCG  < 32 ≤  ATCG