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%	311.6 / NA	82	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 (51/31);  total (51/31)

GGTGCGCTGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGAAAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCATGCG  >  REL606/3762668‑3762813                                                                          |                                                                         ggTGCGCTGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAg                                                                        <  1:675039/76‑1 (MQ=255)    gcgcTGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATg                                                                     <  1:1004915/76‑1 (MQ=255)    gcgcTGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATg                                                                     <  2:1475025/76‑1 (MQ=255)    gcgcTGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATg                                                                     <  2:1150598/76‑1 (MQ=255)    gcgcTGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGATTGAATACGGAAGAGATAGATg                                                                     >  1:368326/1‑76 (MQ=255)     cgcTGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATgg                                                                    >  1:1818175/1‑76 (MQ=255)       cTGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGtg                                                                  >  2:1072392/1‑75 (MQ=255)       cTGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTc                                                                  >  2:874032/1‑76 (MQ=255)       cTGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTc                                                                  >  2:1699034/1‑76 (MQ=255)       cTGGCAAACCCGACGGCAGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGCAGAGATAGATAGTc                                                                  >  1:162085/1‑76 (MQ=255)        tGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCACAGTTTGAATACGGAAGAGATAGATGGTcg                                                                 >  2:685889/1‑76 (MQ=255)        tGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTcg                                                                 <  2:1464869/76‑1 (MQ=255)         ggCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTcgc                                                                >  2:1373098/1‑76 (MQ=255)            aaaCCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTc                                                             >  2:253806/1‑76 (MQ=255)            aaaCCTCACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTc                                                             >  1:1872415/1‑76 (MQ=255)             aaCCTGACGGCGGCAATTANCNCGACGACNTCGAATATTCAAAGTTTGAATNCGNAATAGATAGATGGTCGCGTCt                                                            <  2:300523/76‑1 (MQ=255)                cTGACGGCGGCAATTAACACCACGCCTTNTAATATTCAACGTTTGAATTCNGACGAGATAGATGGTCGCGTCTACa                                                         >  1:291513/1‑76 (MQ=255)                 tGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAg                                                        <  2:1017453/76‑1 (MQ=255)                 tGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAg                                                        <  2:945379/76‑1 (MQ=255)                  gACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAgc                                                       >  2:749935/1‑76 (MQ=255)                     ggcggcAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGcc                                                    >  2:663032/1‑76 (MQ=255)                     ggcggcAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGcc                                                    >  2:277836/1‑76 (MQ=255)                       cggcAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCtt                                                  <  1:1110016/76‑1 (MQ=255)                        ggcAATTAACANCANGACTTCGAATAGTCAAAGTTTGAATACGGAAGAGATAGATGGCTGCGTCTATAGCGCCttt                                                 <  2:318548/76‑1 (MQ=255)                         gcAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTa                                                <  1:665277/76‑1 (MQ=255)                              tAACACCACGACTTCGCATATTCAAAGTTTGAATACGGATGAGATAGATGGTCGCGTATAGAGCGCCTTTGTTCGt                                           >  1:18955/1‑76 (MQ=255)                               aaCACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTc                                          >  1:1653325/1‑76 (MQ=255)                                acacCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCt                                         <  2:936285/76‑1 (MQ=255)                                 caccacGANTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTg                                        >  1:1968761/1‑76 (MQ=255)                                 caccacGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTg                                        >  1:450491/1‑76 (MQ=255)                                 caccacGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTg                                        <  1:943802/76‑1 (MQ=255)                                 caccacGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTg                                        <  2:937452/76‑1 (MQ=255)                                 caccacGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTg                                        >  2:481867/1‑76 (MQ=255)                                 caccacGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTAGTCTg                                        >  2:73450/1‑76 (MQ=255)                                  accacGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGa                                       >  1:1217067/1‑76 (MQ=255)                                  accacGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGa                                       <  1:814621/76‑1 (MQ=255)                                  accacGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGa                                       <  2:930108/76‑1 (MQ=255)                                    cacGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGAcc                                     <  1:818370/76‑1 (MQ=255)                                    cacGACTTCGAATATTCAAAGTTTGAANACGGAAGAAATCGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGAcc                                     >  1:1801155/1‑76 (MQ=255)                                       gACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCt                                  <  1:1900672/76‑1 (MQ=255)                                       gACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCt                                  >  2:1376283/1‑76 (MQ=255)                                       gACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCt                                  >  2:1197709/1‑76 (MQ=255)                                          ttCGAATATTCAAAGTTTGAATAGGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGt                               >  2:1906477/1‑76 (MQ=255)                                          ttCGAATATTCAAAGTTNGNATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGt                               <  1:1086573/76‑1 (MQ=255)                                            caaaTATTCAAAGTTTGAATACGGAAGAGCTAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGa                             <  2:51398/74‑1 (MQ=255)                                             gAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGAc                            >  2:277294/1‑76 (MQ=255)                                              aaTATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGAcc                           <  1:701521/76‑1 (MQ=255)                                               atatTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCg                          >  1:911084/1‑76 (MQ=255)                                               atatTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCg                          >  1:1148453/1‑76 (MQ=255)                                                tatTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTAATTCGTCTGACCGCTCGTGACCgt                         >  2:1493069/1‑76 (MQ=255)                                                 atTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGTCCGCTCGTGACCgtg                        >  1:1693771/1‑76 (MQ=255)                                                 atTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCgtg                        >  2:1093012/1‑76 (MQ=255)                                                 atTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCCCCTTTATTCGTCTGACCGCTCGTGACCgtg                        >  1:38769/1‑76 (MQ=255)                                                   tCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTAATTCGTCTGACCGCTCGTGACCGtgtg                      >  1:197138/1‑76 (MQ=255)                                                    cAAAGTTTGAATAAGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGc                     >  1:1102913/1‑76 (MQ=255)                                                     aaaGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCa                    <  1:371746/76‑1 (MQ=255)                                                     aaaGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCa                    <  2:1966078/76‑1 (MQ=255)                                                     aaaGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCa                    >  2:1123818/1‑76 (MQ=255)                                                     aaaGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCa                    <  2:1434073/76‑1 (MQ=255)                                                      aaGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGTTCGTGACCGTGTGCAt                   <  1:849125/76‑1 (MQ=255)                                                      aaGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCAt                   <  1:1239398/76‑1 (MQ=255)                                                        gTTTGAATACGGAAGAGATNGNTCGTCGCNTCTACAGCGCCTTTATTCGTCNGANCGATCGTGACCGTGTGCATCt                 <  2:291513/76‑1 (MQ=255)                                                        gTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCt                 >  1:381909/1‑76 (MQ=255)                                                        gTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCt                 >  2:1132108/1‑76 (MQ=255)                                                        gTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCCTGACCGTGTGCATCt                 >  1:1698339/1‑76 (MQ=255)                                                         tttGAATACGGATGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGGCTCTg                >  2:71257/1‑76 (MQ=255)                                                         tttGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTg                <  2:1863217/76‑1 (MQ=255)                                                         tttGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTg                <  2:422202/76‑1 (MQ=255)                                                           tGAATACGGANGAAATAGATGNTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGc              >  2:2008113/1‑76 (MQ=255)                                                           tGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGc              >  1:532457/1‑76 (MQ=255)                                                            gAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCg             >  2:1180033/1‑76 (MQ=255)                                                             aaTACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGa            <  2:688880/76‑1 (MQ=255)                                                             aaTACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGa            >  2:939691/1‑76 (MQ=255)                                                             aaTACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGa            >  2:1199263/1‑76 (MQ=255)                                                             aaTACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGa            >  2:572733/1‑76 (MQ=255)                                                              aTACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGCGACCGTGTGCATCTGGCGaa           >  2:177218/1‑76 (MQ=255)                                                               tACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGTTCGTGACCGTGTGCATCTGGCGaac          >  1:326160/1‑75 (MQ=255)                                                               tACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGTGAat          >  2:678313/1‑76 (MQ=255)                                                               tACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAat          <  1:853028/76‑1 (MQ=255)                                                                  ggACGAGATAGATGGTCGCATCTANAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATc       >  1:175255/1‑76 (MQ=255)                                                                   gAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCa      >  2:671808/1‑76 (MQ=255)                                                                   gAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCa      >  1:931171/1‑76 (MQ=255)                                                                    aaGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCAt     >  2:370859/1‑76 (MQ=255)                                                                      gagaTAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCATgc   <  1:1240542/76‑1 (MQ=255)                                                                      gagaTAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCATgc   >  2:486808/1‑76 (MQ=255)                                                                       agatagatGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCATgcg  <  2:1965165/76‑1 (MQ=255)                                                                          |                                                                         GGTGCGCTGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGAAAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCATGCG  >  REL606/3762668‑3762813

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑