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%	159.0 / NA	41	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 (25/16);  total (25/16)

GCGCTGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGAAAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCATGC  >  REL606/3762671‑3762812                                                                       |                                                                        gcgcTGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATg                                                                    <  1:1273981/76‑1 (MQ=255)  cgcTGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATgg                                                                   <  1:505464/76‑1 (MQ=255)  cgcTGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATgg                                                                   >  1:378294/1‑76 (MQ=255)    cTGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTc                                                                 <  1:222624/76‑1 (MQ=255)      ggCAAACCTGACGGCGGCAATTAACACCACGACTTCGACTATTCAAAGTTTGAATACGGAAGAGATAGATGGTcgc                                                               >  2:915489/1‑76 (MQ=255)      ggCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTcgc                                                               >  2:734702/1‑76 (MQ=255)      ggCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTcgc                                                               >  2:50999/1‑76 (MQ=255)      ggCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTcgc                                                               >  2:1219775/1‑76 (MQ=255)          aaCCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCt                                                           <  1:778146/76‑1 (MQ=255)          aaCCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCt                                                           <  2:1087409/76‑1 (MQ=255)          aaCCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCt                                                           <  1:441405/76‑1 (MQ=255)          aaCCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCt                                                           <  1:277232/76‑1 (MQ=255)            ccTGANGACGGCAATTAACACCACGACTACGAATATTCAAAGTTTGAATACGGAAGAGATANATGGTCGCGTCTAc                                                         >  2:1712117/1‑76 (MQ=255)               gACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAgc                                                      >  1:834450/1‑76 (MQ=255)                  ggcggcAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGcc                                                   >  1:1160566/1‑76 (MQ=255)                          ttAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCg                                           >  2:848925/1‑76 (MQ=255)                           tAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGt                                          >  2:187675/1‑76 (MQ=255)                            aaCACCTCGANTACGAATATTNAAAGTTTGAATAAGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTc                                         >  2:1682238/1‑76 (MQ=255)                               accacGACTTCGTATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGa                                      <  1:120314/76‑1 (MQ=255)                               accacGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGa                                      <  2:1651602/76‑1 (MQ=255)                                ccacGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGAc                                     <  1:1207692/76‑1 (MQ=255)                                 cacGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGAcc                                    >  2:936581/1‑76 (MQ=255)                                   cGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGc                                  >  1:1085093/1‑76 (MQ=255)                                   cGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGc                                  >  1:357754/1‑76 (MQ=255)                                             tataCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGCCTACAGCGCCTTTATTCATCTGACCGCTCATTACCgc                        >  2:1664285/1‑75 (MQ=255)                                              atTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCgtg                       >  1:1127720/1‑76 (MQ=255)                                              atTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCgtg                       >  1:558522/1‑76 (MQ=255)                                              atTAAAAGTTTGAATTCGGAAGAGATAGATCGGCGCGTCTACAGCGCCTTTATTCGCCTGTCACCTCGTGACCgtg                       <  1:22417/76‑1 (MQ=255)                                                 cAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGc                    <  1:1024732/76‑1 (MQ=255)                                                      tttGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTg               <  2:336873/76‑1 (MQ=255)                                                      tttGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTg               <  1:1630296/76‑1 (MQ=255)                                                      tttGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTg               <  2:1213257/76‑1 (MQ=255)                                                           aTACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGaa          >  1:228366/1‑76 (MQ=255)                                                              cGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAatat       >  2:337226/1‑76 (MQ=255)                                                              cGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAatat       >  2:627714/1‑76 (MQ=255)                                                              cGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAatat       >  2:654944/1‑76 (MQ=255)                                                              cGGAAGAGATAGATGGTCGCGCCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGCCGAatat       >  2:86311/1‑76 (MQ=255)                                                               ggAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATc      >  2:1196943/1‑76 (MQ=255)                                                                gAAGAGANTGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCa     >  2:1389756/1‑76 (MQ=255)                                                                 aaGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCAt    <  2:665266/76‑1 (MQ=255)                                                                 aaGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCAGACCGCTCNTGACCGTGTGCATCTGGCGAATATCan    <  1:1510417/76‑2 (MQ=255)                                                                  agagATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCATg   >  1:1207089/1‑76 (MQ=255)                                                                   gagaTAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTAGTGACCGTGTGCATCCGGCGAACATCATgc  >  1:24732/1‑76 (MQ=255)                                                                       |                                                                        GCGCTGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGAAAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCATGC  >  REL606/3762671‑3762812

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑