Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,867,700	T→C	T352A (ACC→GCC)	nlpD ←	murein hydrolase activator NlpD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,867,700	0	T	C	100.0%	176.2 / NA	52	T352A (ACC→GCC)	nlpD	murein hydrolase activator NlpD
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (20/32);  total (20/32)

TGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCGCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATTTCCCCTTGTAACGAATTTCAAAATGCAAGCGTGTTGAACTGGTTCCGGTGCTACCCATGGTCGCTATTTTTTGCCCCGCCTTAACTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAG  >  NC_000913/2867569‑2867835                                                                                                                                    |                                                                                                                                        tGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCGCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATTTCCCCTTGTAACGAATTTCAAAATGCAAGCGTGTTGAACTGGTTCCGGCGCTACCCa                                                                                                                                 >  2:295377/1‑140 (MQ=255)  gATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCGCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATTTCCCCTTGTAACGAATTTCAAAATGCAAGCGTGTTGAACTGGTTCCGGCGCTACCCAt                                                                                                                                >  1:396500/1‑140 (MQ=255)  gATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCGCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATTTCCCCTTGTAACGAATTTCAAAATGCAAGCGTGTTGAACTGGTTCCGGCGCTACCCAt                                                                                                                                >  2:193572/1‑140 (MQ=255)   aTCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCGCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATTTCCCCTTGTAACGAATTTCAAAATGCAAGCGTGTTGAACTGGTTCCGGCGCTACCCATg                                                                                                                               <  2:757707/140‑1 (MQ=255)      ccTTGACGGAACATTCAAGCAAAAGCCTGGTTCCGCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATTTCCCCTTGTAACGAATTTCAAAATGCAAGCGTGTTGAACTGGTTCCGGCGCTACCCATGGt                                                                                                                             >  1:781359/1‑139 (MQ=255)      ccTTGACGGAACATTCAAGCAAAAGCCTGGTTCCGCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATTTCCCCTTGTAACGAATTTCAAAATGCAAGCGTGTTGAACTGGTTCCGGCGCTACCCATGGt                                                                                                                             <  2:781359/139‑1 (MQ=255)        ttGACGGAACATTCAAGCAAAAGCCTGGTTCCGCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATTTCCCCTTGTAACGAATTTCAAAATGCAAGCGTGTTGAACTGGTTCCGGCGCTACCCATGGTCGc                                                                                                                          >  2:336222/1‑140 (MQ=255)         tGACGGAACATTCAAGCAAAAGCCTGGTTCCGCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATTTCCCCTTGTAACGAATTTCAAAATGCAAGCGTGTTGAACNGGNTCCGGCNCTACCCATGGTCGCt                                                                                                                         <  1:582643/140‑1 (MQ=255)           aCGGAACATTCAAGCAAAAGCCTGGTTCCGCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATTTCCCCTTGTAACGAATTTCAAAATGCAAGCGTGTTGAACTGGTTCCGGCGCTACCCATGGTCGCTAt                                                                                                                       >  1:695070/1‑140 (MQ=255)              gAACATTCAAGCAAAAGCCTGGTTCCGCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATTTCCCCTTGTAACGAATTTCAAAATGCAAGCGTGTTGAACTGGTTCCGGCGCTACCCATGGTCGCTAtttt                                                                                                                    >  2:380358/1‑140 (MQ=255)               aaCATTCAAGCAAAAGCCTGGTTCCGCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATTTCCCCTTGTAACGAATTTCAAAATGCAAGCGTGTTGAACTGGTTCCGGCGCTACCCATGGTCGCTAttttt                                                                                                                   >  2:162385/1‑140 (MQ=255)                    tCAAGCAAAAGCCTGGTTCCGCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATTTCCCCTTGTACCGAATTTCAAAATGCAAGCGTGTTGAACTGGTTCCGGCGCTACCCATGGTCGCTATTTTTTGccc                                                                                                              <  2:728289/140‑1 (MQ=255)                    tCAAGCAAAAGCCTGGTTCCGCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATTTCCCCTTGTAACGAATTTCAAAATGCAAGCGTGTTGAACTGGTTCCGGCGCTACCCATGGTCGCTATTTTTTGccc                                                                                                              <  2:497206/140‑1 (MQ=255)                    tCAAGCAAAAGCCTGGTTCCGCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATTTCCCCTTGTAACGAATTTCAAAATGCAAGCGTGTTGAACTGGTTCCGGCGCTACCCATGGTCGCTATTTTTTGccc                                                                                                              <  2:396500/140‑1 (MQ=255)                    tCAAGCAAAAGCCTGGTTCCGCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATTTCCCCTTGTAACGAATTTCAAAATGCAAGCGTGTTGAACTGGTTCCGGCGCTACCCATGGTCGCTATTTTTTGccc                                                                                                              <  1:623652/140‑1 (MQ=255)                    tCAAGCAAAAGCCTGGTTCCGCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATTTCCCCTTGTAACGAATTTCAAAATGCAAGCGTGTTGAACTGGTTCCGGCGCTACCCATGGTCGCTATTTTTTGccc                                                                                                              <  2:828808/140‑1 (MQ=255)                    tCAAGCAAAAGCCTGGTTCCGCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATTTCCCCTTGTAACGAATTTCAAAATGCAAGCGTGTTGAACTGGTTCCGGCGCTACCCATGGTCGCTATTTTTTGcc                                                                                                               >  1:499227/1‑139 (MQ=255)                    tCAAGCAAAAGCCTGGTTCCGCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATTTCCCCTTGTAACGAATTTCAAAATGCAAGCGTGTTGAACTGGTTCCGGCGCTACCCATGGTCGCTATTTTTTGcc                                                                                                               <  2:499227/139‑1 (MQ=255)                        gCAAAAGCCTGGTTCCGCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATTTCCCCTTGTAACGAATTTCAAAATGCAAGCGTGTTGAACTGGTTCCGGCGCTACCCATGGTCGCTATTTTTTGCCCCGcc                                                                                                          <  2:332212/140‑1 (MQ=255)                         cAAAAGCCTGGTTCCGCCGATTTATCGCTGCGGCAAATAACGCGGCGGGTTTACGGATTTCCCCTTGTAACGAATTTCAAAATGCAAGCGTGTTGAACTGGTTCCGGCGCTACCCATGGTCGCTATTTTTTGCCCCGCCt                                                                                                         >  1:728032/1‑140 (MQ=255)                         cAAAAGCCTGGTTCCGCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATTTCCCCTTGTAACGAATTTCAAAATGCAAGCGTGTTGAACTGGTTCCGGCGCTACCCATGGTCGCTATTTTTTGCCCCGCCt                                                                                                         >  2:459700/1‑140 (MQ=255)                            aaGCCTGGTTCCGCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATTTCCCCTTGTAACGAATTTCAAAATGCAAGCGTGTTGAACTGGTTCCGGCGCTACCCATGGTCGCTATTTTTTGCCCCGCCTTaa                                                                                                      >  2:794075/1‑140 (MQ=255)                                   gTTCCGCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATTTCCCCTTGTAACGAATTTCAAAATGCAAGCGTGTTGAACTGGTTCCGGCGCTACCCATGGTCGCTATTTTTTGCCCCGCCTTAACTTCttg                                                                                               <  1:465644/140‑1 (MQ=255)                                    ttCCGCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATTTCCCCTTGTAACGAATTTCAAAATGCAAGCGTGTTGAACTGGTTCCGGCGCTACCCATGGTCGCTATTTTTTGCCCCGCCTTAACTTCttgt                                                                                              >  1:806127/1‑140 (MQ=255)                                    ttCCGCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATTTCCCCTTGTAACGAATTTCAAAATGCAAGCGTGTTGAACTGGTTCCGGCGCTACCCATGGTCGCTATTTTTTGCCCCGCCTTAACTTCttgt                                                                                              <  2:259389/140‑1 (MQ=255)                                     tCCGCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATTTCCCCTTGTAACGAATTTCAAAATGCAAGCGTGTTGAACTGGTTCCGGCGCTACCCATGGTCGCTATTTTTTGCCCCGCCTTAACTTCttgtt                                                                                             <  2:485032/140‑1 (MQ=255)                                        gccgATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATTTCCCCTTGTAACGAATTTCAAAATGCAAGCGTGTTGAACTGGTTCCGGCGCTACCCATGGTCGCTATTTTTTGCCCCGCCTTAACTTCTTgttgtt                                                                                          >  1:625512/1‑140 (MQ=255)                                        gccgATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATTTCCCCTTGTAACGAATTTCAAAATGCAAGCGTGTTGAACTGGTTCCGGCGCTACCCATGGTCGCTATTTTTTGCCCCGCCTTAACTTCTTgttgtt                                                                                          >  2:363310/1‑140 (MQ=255)                                              ttATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATTTCCCCTTGTAACGAATTTCAAAATGCAAGCGTGTTGAACTGGTTCCGGCGCTACCCATGGTCGCTATTTTTTGCCCCGCCTTAACTTCTTGTTGTTCCCGGa                                                                                    <  2:625512/140‑1 (MQ=255)                                              ttATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATTTCCCCTTGTAACGAATTTCAAAATGCAAGCGTGTTGAACTGGTTCCGGCGCTACCCATGGTCGCTATTTTTTGCCCCGCCTTAACTTCTTGTTGTTCCCGGa                                                                                    <  1:363310/140‑1 (MQ=255)                                               tATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATTTCCCCTTGTAACGAATTTCAAAATGCAAGCGTGTTGAACTGGTTCCGGCGCTACCCATGGTCGCTATTTTTTGCCCCGCCTTAACTTCTTGTTGTTCCCGGAc                                                                                   <  1:336222/140‑1 (MQ=255)                                                    cTGCGGCAAATAACGCAGCGGGTTTACGGATTTCCCCTTGTAACGAATTTCAAAATGCAAGCGTGTTGAACTGGTTCCGGCGCTACCCATGGTCGTTATTTTTTGCCCCGCCTTAACTTCTTGTTGTTCCCGGACCAGCa                                                                              <  2:206482/140‑1 (MQ=255)                                                    cTGCGGCAAATAACGCAGCGGGTTTACGGATTTCCCCTTGTAACGAATTTCAAAATGCAAGCGTGTTGAACTGGTTCCGGCGCTACCCATGGTCGCTATTTTTTGCCCCGCCTTAACTTCTTGTTGTTCCCGGACCAGCa                                                                              <  2:806127/140‑1 (MQ=255)                                                       cGGCAAATAACGCAGCGGGTTTACGGATTTCCCCTTGTAACGAATTTCAAAATGCAAGCGTGTTGAACTGGTTCCGGCGCTACCCATGGTCGCTATTTTTTGCCCCGCCTTAACTTCTTGTTGTTCCCGGACCAGCATtg                                                                           >  1:710671/1‑140 (MQ=255)                                                               aaCGCGGCGGGTTTACGGATTTCCCCTTGTAACGAATTTCAAAATGCAAGCGTGTTGAACTGGTTCCGGCGCTACCCATGGTCGCTATTTTTTGCCCCGCCTTAACTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTa                                                                   <  2:728032/140‑1 (MQ=255)                                                               aaCGCAGCGGGTTTACGGATTTCCCCTTGTAACGAATTTCAAAATGCAAGCGTGTTGAACTGGTTCCGGCGCTACCCATGGTCGCTATTTTTTGCCCCGCCTTAACTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTa                                                                   <  1:459700/140‑1 (MQ=255)                                                                 cGCAGCGGGTTTACGGATTTCCCCTTGTAACGAATTTCAAAATGCAAGCGTGTTGAACTGGTTCCGGCGCTACCCATGGTCGCTATTTTTTGCCCCGCCTTAACTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATg                                                                 >  2:538584/1‑140 (MQ=255)                                                                      cGGGTTTACGGATTTCCCCTTGTAACGAATTTCAAAATGCAAGCGTGTTGAACTGGTTCCGGCGCTACCCATGGTCGCTATTTTTTGCCCCGCCTTAACTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGt                                                            <  1:295377/140‑1 (MQ=255)                                                                      cGGGTTTACGGATTTCCCCTTGTAACGAATTTCAAAATGCAAGCGTGTTGAACTGGTTCCGGCGCTACCCATGGTCGCTATTTTTTGCCCCGCCTTAACTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGt                                                            <  1:818504/140‑1 (MQ=255)                                                                             aCGGATTTCCCCTTGTAACGAATTTCAAAATGCAAGCGTGTTGAACTGGTTCCGGCGCTACCCATGGTCGCTATTTTTTGCCCCGCCTTAACTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACt                                                     <  2:710671/140‑1 (MQ=255)                                                                              cGGATTTCCCCTTGTAACGAATTTCAAAATGCAAGCGTGTTGAACTGGTTCCGGCGCTACCCATGGTCGCTATTTTTTGCCCCGCCTTAACTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTc                                                    <  2:695070/140‑1 (MQ=255)                                                                              cGGATTTCCCCTTGTAACGAATTTCAAAATGCAAGCGTGTTGAACTGGTTCCGGCGCTACCCATGGTCGCTATTTTTTGCCCCGCCTTAACTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTc                                                    <  1:193572/140‑1 (MQ=255)                                                                              cGGATTTCCCCTTGTAACGAATTTCAAAATGCAAGCGTGTTGAACTGGTTCCGGCGCTACCCATGGTCGCTATTTTTTGCCCCGCCTTAACTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTc                                                    <  2:373927/140‑1 (MQ=255)                                                                                  tttCCCCTTGTAACGAATTTCAAAATGCAAGCGTGTTGAACTGGTTCCGGCGCTACCCATGGTCGCTATTTTTTGCCCCGCCTTAACTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGt                                                <  1:538584/140‑1 (MQ=255)                                                                                    tCCCCTTGTAACGAATTTCAAAATGCAAGCGTGTTGAACTGGTTCCGGCGCTACCCATGGTCGCTATTTTTTGCCCCGCCTTAACTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTaa                                              >  2:69263/1‑140 (MQ=255)                                                                                     ccccTTGTAACGAATTTCAAAATGCAAGCGTGTTGAACTGGTTCCGGCGCTACCCATGGTCGCTATTTTTTGCCCCGCCTTAACTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAat                                             <  1:794075/140‑1 (MQ=255)                                                                                      cccTTGTAACGAATTTCAAAATGCAAGCGTGTTGAACTGGTTCCGGCGCTACCCATGGTCGCTATTTTTTGCCCCGCCTTAACTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAatc                                            <  1:313303/140‑1 (MQ=255)                                                                                            tAACGAATTTCAAAATGCAAGCGTGTTGAACTGGTTCCGGCGCTACCCATGGTCGCTATTTTTTGCCCCGCCTTAACTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCAtt                                      <  1:828343/140‑1 (MQ=255)                                                                                                      cAAAATGCAAGCGTGTTGAACTGGTTCCGGCGCTACCCATGGTCGCTATTTTTTGCCCCGCCTTAACTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTtgatg                            <  2:166401/140‑1 (MQ=255)                                                                                                      cAAAATGCAAGCGTGTTGAACTGGTTCCGGCGCTACCCATGGTCGCTATTTTTTGCCCCGCCTTAACTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTtgatg                            >  2:812585/1‑140 (MQ=255)                                                                                                                   tgtTGAACTGGTTCCGGCGCTACCCATGGTCGCTATTTTTTGCCCCGCCTTAACTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTAc               <  1:162385/140‑1 (MQ=255)                                                                                                                                ccGGCGCTACCCATGGTCGCTATTTTTTGCCCCGCCTTAACTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAg  >  1:822109/1‑140 (MQ=255)                                                                                                                                    |                                                                                                                                        TGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCGCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATTTCCCCTTGTAACGAATTTCAAAATGCAAGCGTGTTGAACTGGTTCCGGTGCTACCCATGGTCGCTATTTTTTGCCCCGCCTTAACTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAG  >  NC_000913/2867569‑2867835

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑