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%	223.6 / NA	58	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 (28/30);  total (28/30)

GGTGCGCTGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGAAAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCATGCG  >  REL606/3762668‑3762813                                                                          |                                                                         ggTGCGCTGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAg                                                                        <  1:217410/76‑1 (MQ=255) ggTGCGCTGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAg                                                                        <  2:619083/76‑1 (MQ=255)  gTGCGCTGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGa                                                                       >  1:1118593/1‑76 (MQ=255)        tGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTcg                                                                 >  1:1402115/1‑76 (MQ=255)          gCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTcgcg                                                               <  1:1315643/76‑1 (MQ=255)           cAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGt                                                              >  2:186361/1‑76 (MQ=255)           cAAACCTGACGGCGGCAATTAACACCACGAATTCGAATACTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGt                                                              >  1:1581926/1‑76 (MQ=255)             aaCCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCt                                                            <  2:366831/76‑1 (MQ=255)             aaCCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCt                                                            <  1:1540784/76‑1 (MQ=255)              aCCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTa                                                           >  2:1834090/1‑76 (MQ=255)               ccTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTAc                                                          >  2:465342/1‑76 (MQ=255)                cTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACa                                                         <  1:369856/76‑1 (MQ=255)                cTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACa                                                         <  1:369843/76‑1 (MQ=255)                 tGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAg                                                        <  1:1172601/76‑1 (MQ=255)                 tGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAg                                                        <  1:582281/76‑1 (MQ=255)                  gACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAgc                                                       >  2:412954/1‑76 (MQ=255)                   aCGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTGGCGTCTACAgcg                                                      <  2:847495/76‑1 (MQ=255)                   aCGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAgcg                                                      <  1:553298/76‑1 (MQ=255)                     ggcggcAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGcc                                                    >  2:1787409/1‑76 (MQ=255)                        tgcAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCttt                                                 >  2:1541846/2‑76 (MQ=255)                        ggcAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCttt                                                 <  1:79957/76‑1 (MQ=255)                         gcAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTa                                                >  1:797707/1‑76 (MQ=255)                           aaTTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTAtt                                              <  1:1212283/76‑1 (MQ=255)                           aaTTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTAtt                                              >  1:477966/1‑76 (MQ=255)                           aaTTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTAtt                                              <  1:1212305/76‑1 (MQ=255)                            aTTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTc                                             >  1:1354278/1‑76 (MQ=255)                             ttAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCg                                            <  1:588890/76‑1 (MQ=255)                              tAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGt                                           >  2:946471/1‑76 (MQ=255)                                  accacGACTTCAAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGa                                       >  1:55931/1‑76 (MQ=255)                                         cTTCGAATATTCAGAGTTTGNATACGGAAGTGATAGNTGGTCGCGTCTACTGTGCCTTGATTCGTCTGACCGCTCg                                <  2:2026640/76‑1 (MQ=255)                                         cTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCg                                <  1:437479/76‑1 (MQ=255)                                         cTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCg                                >  1:1500342/1‑76 (MQ=255)                                           tCGAATATTCAAAGTTTGAATACGGAANAGATAGATGGTAGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTg                              >  1:1782664/1‑76 (MQ=255)                                            cGAATATTCAAAGTTTGAATACGGAAGCGATCGANGGTCCCGNCTNCANCGCCTTTATTCGTCTGACCGCTCGTGa                             >  1:1770144/1‑76 (MQ=255)                                            cGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGa                             <  2:1956016/76‑1 (MQ=255)                                             taaTATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTATGACAGCTCGTGAc                            >  2:128379/2‑76 (MQ=255)                                                  ttCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCgtgt                       >  1:829255/1‑76 (MQ=255)                                                  ttCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCgtgt                       <  2:1708080/76‑1 (MQ=255)                                                   tCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCTTGACCGtgtg                      <  2:962206/76‑1 (MQ=255)                                                    cAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCTTGACCGTGTGc                     <  1:54507/76‑1 (MQ=255)                                                     aaaGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCa                    >  2:1369270/1‑76 (MQ=255)                                                       aGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGGATc                  <  2:931584/76‑1 (MQ=255)                                                       aGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATc                  <  1:1037177/76‑1 (MQ=255)                                                        gTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCt                 <  1:723571/76‑1 (MQ=255)                                                        gTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCt                 <  1:1164910/76‑1 (MQ=255)                                                         tttGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTg                <  1:754353/76‑1 (MQ=255)                                                         tttGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTg                <  1:1320930/76‑1 (MQ=255)                                                         tttGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTg                <  1:1559455/76‑1 (MQ=255)                                                          ttGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTgg               >  1:781077/1‑76 (MQ=255)                                                          ttGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTgg               >  1:139039/1‑76 (MQ=255)                                                             aaTACGGAAGAGCTAGATGGTCGGGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGNCCGTGTGCATCTGGCGa            <  1:258037/76‑1 (MQ=255)                                                             aaTACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGa            >  2:1215398/1‑76 (MQ=255)                                                              aTACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGaa           >  2:957357/1‑76 (MQ=255)                                                               tACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAat          <  1:1124602/76‑1 (MQ=255)                                                                aCGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATCCGTCTGACCGCTCGTGAACGTGTGCATCTCGCAAatg         >  2:1987692/1‑75 (MQ=255)                                                                 cGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAatat        >  2:496465/1‑76 (MQ=255)                                                                 cGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAatat        >  2:1749385/1‑76 (MQ=255)                                                                  ggAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATc       <  2:411698/76‑1 (MQ=255)                                                                  ggAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATc       >  2:1972959/1‑76 (MQ=255)                                                                       agatagatGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCATgcg  >  1:1625799/1‑76 (MQ=255)                                                                          |                                                                         GGTGCGCTGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGAAAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCATGCG  >  REL606/3762668‑3762813

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑