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%	155.6 / NA	42	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 (24/18);  total (24/18)

GTGCGCTGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGAAAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCATGC  >  REL606/3762669‑3762812                                                                         |                                                                        gTGCGCTGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGa                                                                      >  1:59110/1‑76 (MQ=255)  tGCGCTGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGagatagat                                                                     <  2:819274/76‑1 (MQ=255)   gcgcTGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATg                                                                    <  1:214811/76‑1 (MQ=255)      cTGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTc                                                                 <  1:638572/76‑1 (MQ=255)      cTGGCAAACCTGACGGCGGCAATTAACAACACGACTCGGAATATTCANAGATTGAATACGGAAGAGATAGATGGTc                                                                 >  1:115020/1‑76 (MQ=255)       tGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTcg                                                                <  1:822964/76‑1 (MQ=255)        ggCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTcgc                                                               <  1:932889/76‑1 (MQ=255)          cAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGt                                                             >  1:666857/1‑76 (MQ=255)           aaaCCTGACGGCGGCACTTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTc                                                            >  2:311741/1‑76 (MQ=255)           aaaCCTGACGGCGGCAATTAGCTCCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTc                                                            >  1:8251/1‑76 (MQ=255)           aaaCCTGACGGCGGCAATTAACACCACGACTTCNAATATTCAAAGTTTGAATACGGNAGAGATAGTTNGTCGCGTc                                                            >  2:1009419/1‑76 (MQ=255)              ccTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTAc                                                         <  2:796966/76‑1 (MQ=255)                tGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAg                                                       >  1:268108/1‑76 (MQ=255)                 gACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAgc                                                      <  1:845346/76‑1 (MQ=255)                  aCGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAgcg                                                     >  1:772092/1‑76 (MQ=255)                        gcAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTa                                               <  2:730153/76‑1 (MQ=255)                         cAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTAt                                              >  1:963413/1‑76 (MQ=255)                          aaTTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTAtt                                             >  1:1181187/1‑76 (MQ=255)                            ttAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCg                                           >  2:477043/1‑76 (MQ=255)                            ttAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCg                                           <  1:1177065/76‑1 (MQ=255)                              aaCACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTc                                         >  2:972233/1‑76 (MQ=255)                               acacCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCt                                        >  2:870715/1‑76 (MQ=255)                                caccacGACTTCGATTATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTg                                       <  1:760854/76‑1 (MQ=255)                                       aCTTCGAATATTCANAGTTTGAATACGGAAGAGANAGATGCTCNCGTCTACAGCGCCTTTATTCGTCTGACCGCTc                                <  2:990629/76‑1 (MQ=255)                                         ttCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGt                              >  2:2069/1‑76 (MQ=255)                                         ttCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGt                              <  2:32747/76‑1 (MQ=255)                                         ttCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGt                              >  1:337324/1‑76 (MQ=255)                                          tCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTg                             <  1:717512/76‑1 (MQ=255)                                          tCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCCCGCGTg                             <  1:76990/76‑1 (MQ=255)                                           cGAAGATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCTCCTTTATTCGTCTGACCGGTCGNGa                            >  2:1142103/1‑76 (MQ=255)                                             aaTATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGAcc                          >  1:426524/1‑76 (MQ=255)                                               tatTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCgt                        >  2:637117/1‑76 (MQ=255)                                                   cAAAGTTTGAATACGGAAGAAATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGc                    >  1:3447/1‑76 (MQ=255)                                                       gTTTGAATNCGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCt                <  1:1060208/76‑1 (MQ=255)                                                        tttGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTg               <  2:64389/76‑1 (MQ=255)                                                        tttGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTg               >  2:925988/1‑76 (MQ=255)                                                              tACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAat         <  2:822507/76‑1 (MQ=255)                                                               aCGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAata        >  1:1044142/1‑76 (MQ=255)                                                               aCGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAata        >  2:767219/1‑76 (MQ=255)                                                                cGGAAGAGATAGGTGGTCGCGTCTACAGCGCCTTTATTCGGCTGACCGCGCGGGACCGTGTGCATCTGGCGAatat       <  2:886921/76‑1 (MQ=255)                                                                cGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAatat       <  2:886902/76‑1 (MQ=255)                                                                 ggAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATc      >  2:785183/1‑76 (MQ=255)                                                                    agagATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCATg   <  1:904078/76‑1 (MQ=255)                                                                     gagaTAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATGTCATgc  >  1:1103605/1‑76 (MQ=255)                                                                         |                                                                        GTGCGCTGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGAAAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCATGC  >  REL606/3762669‑3762812

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑