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%	127.4 / 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 (19/18);  total (19/18)

GTGCGCTGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGAAAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCA  >  REL606/3762669‑3762809                                                                         |                                                                     gTGCGCTGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGa                                                                   <  1:501086/76‑1 (MQ=255)      cTGGCAAACCTGACGGCTGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGGCGGTc                                                              <  1:1119193/76‑1 (MQ=255)          cAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGt                                                          >  1:560901/1‑76 (MQ=255)          cAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGt                                                          >  1:944866/1‑76 (MQ=255)           aaaCCTCACGNTGGCAATTAANACCACGACTTCGTATATTCAAAGTTTGACTACGGAAGAGATAGATGGTCGCGTc                                                         >  2:1190946/1‑76 (MQ=255)               cTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGATATAGATGGTCGCGTCTACa                                                     <  1:1032887/76‑1 (MQ=255)               cTGACGGCGGCAATAACCACCACGACTTCGTATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACa                                                     <  1:24422/76‑1 (MQ=255)                    ggcggcAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGcc                                                >  1:329047/1‑76 (MQ=255)                      cggcAATTAACACCACGACTTCGAATAGTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTGCAGCGCCtt                                              <  2:425074/76‑1 (MQ=255)                        gcAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTa                                            <  2:522256/76‑1 (MQ=255)                        gcAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTa                                            >  1:820675/1‑76 (MQ=255)                        gcAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTa                                            >  1:890843/1‑76 (MQ=255)                          aaTTAACANCACGACTTCGAATATTCAAAGTTTTGCTACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTAtt                                          <  2:199697/76‑1 (MQ=255)                          aaTTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTAtt                                          <  2:378510/76‑1 (MQ=255)                           aTTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTc                                         >  2:617600/1‑76 (MQ=255)                            ttAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCg                                        >  1:881842/1‑76 (MQ=255)                                   cacGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGAcc                                 >  2:1159237/1‑76 (MQ=255)                                        cTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCg                            <  2:551676/76‑1 (MQ=255)                                        cTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCg                            <  1:1097281/76‑1 (MQ=255)                                          tCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTg                          <  2:1036611/76‑1 (MQ=255)                                          tCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTg                          <  1:930279/76‑1 (MQ=255)                                          tCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTg                          >  1:331986/1‑76 (MQ=255)                                             aaTATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGAcc                       >  1:931140/1‑76 (MQ=255)                                             aaTATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCATGAcc                       >  2:580346/1‑76 (MQ=255)                                               tatTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGNCCGCTCGCGACCgt                     <  1:82370/76‑1 (MQ=255)                                               tatTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCgt                     <  1:752942/76‑1 (MQ=255)                                                atTCAAANTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGCGAACgtg                    >  2:975687/1‑76 (MQ=255)                                                 ttCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCgtgt                   <  2:395953/76‑1 (MQ=255)                                                  tCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGtgtg                  <  2:1137506/76‑1 (MQ=255)                                                       gTTTGAATACGGAAGAGATAGATGGTCGCGTCTACGGCGCCTATATTCGTCTGACCGCTCGTGACCGTGTGCATCt             <  1:957617/76‑1 (MQ=255)                                                        tttGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTg            <  2:1040504/76‑1 (MQ=255)                                                          tGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGc          >  2:996381/1‑76 (MQ=255)                                                           gAATACGGAAGCGATAGATGGTCGCGTNTACAGCGNNTTTATACGTCTGACCGCTCGTGACCGTGTGCATCTGGCg         >  1:1195188/1‑76 (MQ=255)                                                             aTACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGaa       >  1:262481/1‑76 (MQ=255)                                                              tACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAat      >  1:772456/1‑76 (MQ=255)                                                               aCGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAata     >  2:336322/1‑76 (MQ=255)                                                                  gAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCa  >  2:68811/1‑76 (MQ=255)                                                                         |                                                                     GTGCGCTGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGAAAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCA  >  REL606/3762669‑3762809

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑