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%	126.6 / NA	34	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 (21/13);  total (21/13)

GCTGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGAAAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCAT  >  REL606/3762673‑3762810                                                                     |                                                                      gcTGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATGCAAAGTTTGAATACGGAAGAGATAGCTGGt                                                                >  1:982797/1‑76 (MQ=255)  cTGGCAAACCTGACGGCGGCAATTAACGCCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTc                                                               >  1:104703/1‑76 (MQ=255)  cTGGCAAACCTGACGGCGGCAATTAACACCACGGCTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTc                                                               <  1:697345/76‑1 (MQ=255)  cTGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTc                                                               >  2:315883/1‑76 (MQ=255)       aaaCCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTAAATACGGAAGAGATAGATGGTCGCATc                                                          >  1:512086/1‑76 (MQ=255)        aaCCTGACGGCGGCAACTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCt                                                         <  2:441212/76‑1 (MQ=255)        aaCCTGACGGCGACAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCt                                                         >  2:156965/1‑76 (MQ=255)          ccTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTAc                                                       <  1:1049242/76‑1 (MQ=255)           cTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACa                                                      >  1:193061/1‑76 (MQ=255)            tGACGGCGGCAATTAACAACACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAg                                                     <  1:824718/76‑1 (MQ=255)                     cAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTAt                                            >  1:786881/1‑76 (MQ=255)                      aaTTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTAtt                                           <  1:25375/76‑1 (MQ=255)                        ttAACACCACGACTTCGAATATTCAAAGTTTGAATACTGAAGAGATAGATGGTCGCGTCTACAGCGTCTTTATTCg                                         <  1:760928/76‑1 (MQ=255)                        ttAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTGCACAGCCCCTTTATTCg                                         >  1:299051/1‑76 (MQ=255)                         tAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGCGATAGATGGTCGCGTCTACCGCGCCTTTATTCGt                                        >  1:900183/1‑76 (MQ=255)                         tAACACCAAGACTTCGAATATTCAAAGTTTGAATACGGAAGANATAGATGGTCGCGTCTACAGCGCCTTTATTCGt                                        >  1:868262/1‑76 (MQ=255)                                acGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCg                                 <  1:575138/76‑1 (MQ=255)                                  gACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTCTATTCGTCTGACCGCt                               >  2:726969/1‑76 (MQ=255)                                      tCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCTCTCGTg                           <  1:156699/76‑1 (MQ=255)                                         aaTATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGAcc                        >  2:307791/1‑76 (MQ=255)                                         aaTATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGAcc                        >  2:241852/1‑76 (MQ=255)                                              tCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGtgtg                   <  1:241977/76‑1 (MQ=255)                                                 aaGTTTGAATACGGAAGAGATAGATGATCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCAt                >  1:535006/1‑76 (MQ=255)                                                   gTTTGAAAACGGAAGAGATAGATGGACGCGTCTANAGCGCCTTTATTCGTCNGTTCGCTCGTGACCGTNTGCATCt              >  2:961022/1‑76 (MQ=255)                                                    tttGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTg             <  2:1026599/76‑1 (MQ=255)                                                    tttGAATACGGAAGAGATAGACGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTg             <  2:906083/76‑1 (MQ=255)                                                      tGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGc           >  2:35368/1‑76 (MQ=255)                                                      tGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGc           >  2:624721/1‑76 (MQ=255)                                                      tGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTATGACCGCTCGTGACCGTGTGCATCTGGc           >  2:598100/1‑76 (MQ=255)                                                       gAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCg          >  1:976389/1‑76 (MQ=255)                                                          tACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAat       >  2:467763/1‑76 (MQ=255)                                                           aCGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAata      >  2:21716/1‑76 (MQ=255)                                                           aCGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAata      >  2:226788/1‑76 (MQ=255)                                                             ggAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATc    <  1:487227/76‑1 (MQ=255)                                                               aaGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCAt  <  1:653996/76‑1 (MQ=255)                                                                     |                                                                      GCTGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGAAAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCAT  >  REL606/3762673‑3762810

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑