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%	231.3 / NA	61	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 (33/28);  total (33/28)

TGCGCTGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGAAAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCATG  >  REL606/3762670‑3762811                                                                        |                                                                       tGCGCTGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGagatagat                                                                    >  1:771045/1‑76 (MQ=255) tGCGCTGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGagatagat                                                                    <  1:812237/76‑1 (MQ=255) tGCGCGGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGagatagat                                                                    <  2:13391/76‑1 (MQ=255)    gcTGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGt                                                                 <  1:545940/76‑1 (MQ=255)      tGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTcg                                                               <  2:1555452/76‑1 (MQ=255)       ggCAAACCTGACGGCGGCAATTAACACCACGACTTCNAATATTCGAAGTTTGCATACGGAAGAGATAGATGNTcgc                                                              >  1:186399/1‑76 (MQ=255)       ggCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTcgc                                                              >  2:669512/1‑76 (MQ=255)         cAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGt                                                            <  2:584166/76‑1 (MQ=255)         cAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGt                                                            <  2:344578/76‑1 (MQ=255)          aaaCCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAAGACGGACGAGATAGATGGTCGCGTc                                                           >  1:1519937/1‑76 (MQ=255)           aaCCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCt                                                          >  2:766947/1‑76 (MQ=255)           aaCCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCt                                                          <  1:569463/76‑1 (MQ=255)            gccTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTa                                                         <  2:575796/75‑1 (MQ=255)              cTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACa                                                       <  1:1167041/76‑1 (MQ=255)              cTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACa                                                       <  1:736081/76‑1 (MQ=255)                 aCGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAgcg                                                    <  1:960752/76‑1 (MQ=255)                 aCGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAgcg                                                    >  1:756424/1‑76 (MQ=255)                  cggcggCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAgcgc                                                   >  1:1131799/1‑76 (MQ=255)                     cggcAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCtt                                                >  1:1370762/1‑76 (MQ=255)                     cggcAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCtt                                                <  1:1571688/76‑1 (MQ=255)                        cAATTAACACCACGACTTCGAATATTCAAAGTTTGACTACGGAAGAGATAGATGGTCGCGTCTACAGNGCCTTTAt                                             >  1:1414254/1‑76 (MQ=255)                        cAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTAt                                             <  2:332186/76‑1 (MQ=255)                        cAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTAt                                             <  2:341064/76‑1 (MQ=255)                        cAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTAt                                             >  2:727360/1‑76 (MQ=255)                        cAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTAt                                             >  1:1092366/1‑76 (MQ=255)                        cAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTAt                                             >  1:613579/1‑76 (MQ=255)                         aaTTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTAtt                                            <  2:971002/76‑1 (MQ=255)                         aaTTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTAtt                                            >  2:474079/1‑76 (MQ=255)                         aaTTAACACCACGACTTCGAATATTAAAAGTATGAATACTNNAGAGATAGATNNTCGCGTCTACAGCGTCTTTAtt                                            >  1:1447400/1‑76 (MQ=255)                          aTTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTc                                           >  1:1141038/1‑76 (MQ=255)                          aTTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTc                                           >  1:1251775/1‑76 (MQ=255)                           ttAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCg                                          <  2:138784/76‑1 (MQ=255)                            tAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGt                                         >  2:290611/1‑76 (MQ=255)                              acacCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCt                                       <  1:647089/76‑1 (MQ=255)                              acacCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCt                                       <  2:973410/76‑1 (MQ=255)                               caccacGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTg                                      >  2:1108262/1‑76 (MQ=255)                               caccacGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTg                                      <  2:574686/76‑1 (MQ=255)                                 ccacGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGAc                                    >  1:1205434/1‑76 (MQ=255)                                  cacGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGAcc                                   <  1:304816/76‑1 (MQ=255)                                    cGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGc                                 >  1:216769/1‑76 (MQ=255)                                       cTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCg                              >  2:131106/1‑76 (MQ=255)                                           gAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGAc                          >  2:1170071/1‑76 (MQ=255)                                           gAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGAc                          >  1:1027589/1‑76 (MQ=255)                                            aaTATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATNCGTCTGACCGCTCGTGAcc                         <  1:1506087/76‑1 (MQ=255)                                              tatTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCgt                       <  1:881572/76‑1 (MQ=255)                                              tatTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCgt                       >  1:408647/1‑76 (MQ=255)                                               atTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCgtg                      >  1:718407/1‑76 (MQ=255)                                                 tCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGtgtg                    <  1:533885/76‑1 (MQ=255)                                                  cAAAGTTTGAATACGGAAGAGATAGGTGNTCGCGTCTATTGCGCCTTGATTCGTCTGACCGCTCGTGACCGTGTGc                   <  1:143440/76‑1 (MQ=255)                                                  cAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGc                   >  1:1122053/1‑76 (MQ=255)                                                  cAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGc                   <  2:674742/76‑1 (MQ=255)                                                   aaaGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCa                  >  2:691769/1‑76 (MQ=255)                                                     aGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATc                <  1:578255/76‑1 (MQ=255)                                                        ttGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCC‑TTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGc            <  2:1496126/76‑1 (MQ=255)                                                         tGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGc            >  2:1166248/1‑76 (MQ=255)                                                          gAATACGGAAGAGATAGCTGGTCGCCTCTACAGCGCCTTTATTCGTCTGATCGCTCGTGACCGTATGCCACTGNCg           >  2:1517920/1‑76 (MQ=255)                                                          gAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCg           >  1:1334937/1‑76 (MQ=255)                                                            aTACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGaa         >  1:411658/1‑76 (MQ=255)                                                            aTACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGaa         >  2:179019/1‑76 (MQ=255)                                                               cGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGGGCATCTGGCGAatat      >  2:113095/1‑76 (MQ=255)                                                                ggAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATc     <  1:1363452/76‑1 (MQ=255)                                                                 gAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCa    >  2:141783/1‑76 (MQ=255)                                                                  aaGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCAt   <  2:1027589/76‑1 (MQ=255)                                                                   agagATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACTGCTCGTGACCGTGTGCATCTGGCGAATATCATg  <  2:1392051/76‑1 (MQ=255)                                                                        |                                                                       TGCGCTGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGAAAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCATG  >  REL606/3762670‑3762811

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑