Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	2,862,125	A→G	intergenic (‑13/+127)	nlpD ← / ← pcm	murein hydrolase activator NlpD/protein‑L‑isoaspartate O‑methyltransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	2,862,125	0	A	G	100.0%	129.2 / NA	36	intergenic (‑13/+127)	nlpD/pcm	murein hydrolase activator NlpD/protein‑L‑isoaspartate O‑methyltransferase
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (16/20);  total (16/20)

ATTAACGGAGCTGACCGGTGCCGGTGGATTTGAAGTGTCAGAACAGCCTGCCAGCCATAGCGAAACCAGTGACAAAGCCGCAATGCGGCGAACGGTGAATTTTGGGCTTCCCGCGCTCATTTATCCCCCAGGAAAAATTGGTTAATAACCAGTGACATAATTACCGTGCAAGGCACCCTACTGAACACTGGAAAAGATGTTCACGATACGCTGACCTGCGGCAAAATAACCAGGAAAAATCCAGGTATTTCCTCACGTTTTAAGC  >  NZ_CP009273/2861993‑2862257                                                                                                                                     |                                                                                                                                     aTTAACGGAGCTGACCGGTGCCGGTGGATTTGAAGTGTCAGAACAGCCTGCCAGCCATAGCGAAACCAGTGACAAAGCCGCAATGCGGCGAACGGTGAATTTTGGGCTTCCCGCGCTCATTTATCCCCCAGGGAAAAtt                                                                                                                                <  2:769235/139‑1 (MQ=255)  ttAACGGAGCTGACCGGTGCCGGTGGATTTGAAGTGTCAGAACAGCCTGCCAGCCATAGCGAAACCAGTGACAAAGCCGCAATGCGGCGAACGGTGAATTTTGGGCTTCCCGCGCTCATTTATCCCCCAGGGAAAATTg                                                                                                                               >  1:199799/1‑139 (MQ=255)   tAACGGAGCTGACCGGTGCCGGTGGATTTGAAGTGTCAGAACAGCCTGCCAGCCATAGCGAAACCAGTGACAAAGCCGCAATGCGGCGAACGGTGAATTTTGGGCTTCCCGCGCTCATTTATCCCCCAGGGAAAATTgg                                                                                                                              >  1:562069/1‑139 (MQ=255)       ggAGCTGACCGGTGCCGGTGGATTTGAAGTGTCAGAACAGCCTGCCAGCCATAGCGAAACCAGTGACAAAGCCGCAATGCGGCGAACGGTGAATTTTGGGCTTCCCGCGCTCATTTATCCCCCAGGGAAAATTGGTtaa                                                                                                                          >  1:275622/1‑139 (MQ=255)         aGCTGACCGGTGCCGGTGGATTTGAAGTGTCAGAACAGCCTGCCAGCCATAGCGAAACCAGTGACAAAGCCGCAATGCGGCGAACGGTGAATTTTGGGCTTCCCGCGCTCATTTATCCCCCAGGGAAAATTGGTtaat                                                                                                                         >  2:273769/1‑138 (MQ=255)              aCCGGTGCCGGTGGATTTGAAGTGTCAGAACAGCCTGCCAGCCATAGCGAAACCAGTGACAAAGCCGCAATGCGGCGAACGGTGAATTTTGGGCTTCCCGCGCTCATTTATCCCCCAGGGAAAATTGGTTAATAACCa                                                                                                                    <  2:408536/138‑1 (MQ=255)              aCCGGTGCCGGTGGATTTGAAGTGTCAGAACAGCCTGCCAGCCATAGCGAAACCAGTGACAAAGCCGCAATGCGGCGAACGGTGAATTTTGGGCTTCCCGCGCTCATTTATCCCCCAGGGAAAATTGGTTAATAACCAg                                                                                                                   >  1:88964/1‑139 (MQ=255)               ccggtgcctgtgGATTTGAAGTGTCAGAACAGCCTGCCAGCCATAGCGAAACCAGTGACAAAGCCGCAATGCGGCGAACGGTGAATTTTGGGCTTCCCGCGCTCATTTATCCCCCAGGGAAAATTGGTTAATAACCAGt                                                                                                                  <  2:815718/139‑1 (MQ=255)               ccggtgccggtgGATTTGAAGTGTCAGAACAGCCTGCCAGCCATAGCGAAACCAGTGACAAAGCCGCAATGCGGCGAACGGTGAATTTTGGGCTTCCCGCGCTCATTTATCCCCCAGGGAAAATTGGTTAATAACCAGt                                                                                                                  <  2:275622/139‑1 (MQ=255)                 ggtgccggtgGATTTGAAGTGTCAGAACAGCCTGCCAGCCATAGCGAAACCAGTGACAAAGCCGCAATGCGGCGAACGGTGAATTTTGGGCTTCCCGCGCTCATTTATCCCCCAGGGAAAATTGGTTAATAACCAGTGa                                                                                                                <  1:350524/139‑1 (MQ=255)                     ccggtgGATTTGAAGTGTCAGAACAGCCTGCCAGCCATAGCGAAACCAGTGACAAAGCCGCAATGCGGCGAACGGTGAATTTTGGGCTTCCCGCGCTCATTTATCCCCCAGGGAAAATTGGTTAATAACCAGTGACAt                                                                                                             <  2:562069/138‑1 (MQ=255)                        gtgGATTTGAAGTGTCAGAACAGCCTGCCAGCCATAGCGAAACCAGTGACAAAGCCGCAATGCGGCGAACGGTGAATTTTGGGCTTCCCGCGCTCATTTATCCCCCAGGGAAAATTGGTTAATAACCAGTGACATAAt                                                                                                          >  1:634410/1‑138 (MQ=255)                               tGAAGTGTCAGAACAGCCTGCCAGCCATAGCGAAACCAGTGACAAAGCCGCAATGCGGCGAACGGTGAATTTTGGGCTTCCCGCGCTCATTTATCCCCCAGGGAAAATTGGTTAATAACCAGTGACATAATTACCGTg                                                                                                   <  2:56463/138‑1 (MQ=255)                                  aGTGTCAGAACAGCCTGCCAGCCATAGCGAAACCAGTGACAAAGCCGCAATGCGGCGAACGGTGAATTTTGGGCTTCCCGCGCTCATTTATCCCCCAGGGAAAATTGGTTAATAACCAGTGACATAATTACCGTGCAAg                                                                                               <  1:64965/139‑1 (MQ=255)                                   gtgtCAGAACAGCCTGCCAGCCATAGCGAAACCAGTGACAAAGCCGCAATGCGGCGAACGGTGAATTTTGGGCTTCCCGCGCTCATTTATCCCCCAGGGAAAATTGGTTAATAACCAGTGACATAATTACCGTGCAAgg                                                                                              <  1:367754/139‑1 (MQ=255)                                      tCAGAACAGCCTGCCAGCCATAGCGAAACCAGTGACAAAGCCGCAATGCGGCGAACGGTGAATTTTGGGCTTCCCGCGCTCATTTATCCCCCAGGGAAAATTGGTTAATAACCAGTGACATAATTACCGTGCAAGGCa                                                                                            <  2:249300/138‑1 (MQ=255)                                              gCCTGCCAGCCATAGCGAAACCAGTGACAAAGCCGCAATGCGGCGAACGGTGAATTTTGGGCTTCCCGCGCTCATTTATCCCCCAGGGAAAATTGGTTAATAACCAGTGACATAATTACCGTGCAAGGCACCCTACTg                                                                                    >  1:629219/1‑138 (MQ=255)                                              gCCTGCCAGCCATAGCGAAACCAGTGACAAAGCCGCAATGCGGCGAACGGTGAATTTTGGGCTTCCCGCGCTCATTTATCCCCCAGGGAAAATTGGTTAATAACCAGTGACATAATTACCGTGCAAGGCACCCTACTg                                                                                    >  1:250298/1‑138 (MQ=255)                                               ccTGCCAGCCATAGCGAAACCAGTGACAAAGCCGCAATGCGGCGAACGGTGAATTTTGGGCTTCCCGCGCTCATTTATCCCCCAGGGAAAATTGGTTAATAACCAGTGACATAATTACCGTGCAAGGCACCCTACTGaa                                                                                  >  2:702544/1‑139 (MQ=255)                                                cTGCCAGCCATAGCGAAACCAGTGACAAAGCCGCAATGCGGCGAACGGTGAATTTTGGGCTTCCCGCGCTCATTTATCCCCCAGGGAAAATTGGTTAATAACCAGTGACATAATTACCGTGCAAGGCACCCTACTGAac                                                                                 <  1:847837/139‑1 (MQ=255)                                                         aTAGCGAAACCAGTGACAAAGCCGCAATGCGGCGAACGGTGAATTTTGGGCTTCCCGCGCTCATTTATCCCCCAGGGAAAAt                                                                                                                                 <  2:190271/82‑1 (MQ=255)                                                         aTAGCGAAACCAGTGACAAAGCCGCAATGCGGCGAACGGTGAATTTTGGGCTTCCCGCGCTCATTTATCCCCCAGGGAAAAt                                                                                                                                 >  1:190271/1‑82 (MQ=255)                                                         aTAGCGAAACCAGTGACAAAGCCGCAATGCGGCGAACGGTGAATTTTGGGCTTCCCGCGCTCATTTATCCCCCAGGGAAAATTGGTTAATAACCAGTGACATAATTACCGTGCAAGGCACCCTACTGAACACTGGaa                                                                          >  2:831699/1‑137 (MQ=255)                                                           aGCGAAACCAGTGACAAAGCCGCAATGCGGCGAACGGTGAATTTTGGGCTTCCCGCGCTCATTTATCCCCCAGGGAAAATTGGTTAATAACCAGTGACATAATTACCGTGCAAGGCACCCTACTGAACACTGGaa                                                                          >  1:34852/1‑135 (MQ=255)                                                                   cAGTGACAAAGCCGCAATGCGGCGAACGGTGAATTTTGGGCTTCCCGCGCTCATTTATCCCCCAGGGAAAATTGGTTAATAACCAGTGACATAATTACCGTGCAAGGCACCCTACTGAACACTGGAAAAGATGTTCACg                                                              <  2:250298/139‑1 (MQ=255)                                                                      tGACAAAGCCGCAATGCGGCGAACGGTGAATTTTGGGCTTCCCGCGCTCATTTATCCCCCAGGGAAAATTGGTTAATAACCAGTGACATAATTACCGTGCAAGGCACCCTACTGAacac                                                                               <  1:7777/119‑1 (MQ=255)                                                                      tGACAAAGCCGCAATGCGGCGAACGGTGAATTTTGGGCTTCCCGCGCTCATTTATCCCCCAGGGAAAATTGGTTAATAACCAGTGACATAATTACCGTGCAAGGCACCCTACTGAacac                                                                               >  2:7777/1‑119 (MQ=255)                                                                      tGACAAAGCCGCAATGCGGCGAACGGTGAATTTTGGGCTTCCCGCGCTCATTTATCCCCCAGGGAAAATTGGTTAATAACCAGTGACATAATTACCGTGCAAGGCACCCTACTGAACACTGGAAAAGATGTTCACGATa                                                           >  1:33011/1‑139 (MQ=255)                                                                          aaaGCCGCAATGCGGCGAACGGTGAATTTTGGGCTTCCCGCGCTCATTTATCCCCCAGGGAAAATTGGTTAATAACCAGTGACATAATTACCGTGCAAGGCACCCTACTGAACACTGGAAAAGATGTTCACGATACGCt                                                       <  2:796462/139‑1 (MQ=255)                                                                             gCCGCAATGCGGCGAACGGTGAATTTTGGGCTTCCCGCGCTCATTTATCCCCCAGGGAAAATTGGTTAATAACCAGt                                                                                                                  <  2:3555/77‑1 (MQ=255)                                                                             gCCGCAATGCGGCGAACGGTGAATTTTGGGCTTCCCGCGCTCATTTATCCCCCAGGGAAAATTGGTTAATAACCAGt                                                                                                                  >  1:3555/1‑77 (MQ=255)                                                                                gCAATGCGGCGAACGGTGAATTTTGGGCTTCCCGCGCTCATTTATCCCCCAGGGAAAATTGGTTAATAACCAGTGACATAATTACCGTGCAAGGCACCCTACTGAacac                                                                               >  2:367880/1‑109 (MQ=255)                                                                                gCAATGCGGCGAACGGTGAATTTTGGGCTTCCCGCGCTCATTTATCCCCCAGGGAAAATTGGTTAATAACCAGTGACATAATTACCGTGCAAGGCACCCTACTGAacac                                                                               <  1:367880/109‑1 (MQ=255)                                                                                       ggcgAACGGTGAATTTTGGGCTTCCCGCGCTCATTTATCCCCCAGGGAAAATTGGTTAATAACCAGTGACATAATTACCGTGCAAGGCACCCTACTGAACACTGGAAAAGATGTTCACGATACGCTGACCTGCGGCaaa                                          <  2:634410/139‑1 (MQ=255)                                                                                                                              ccccAGGGAAAATTGGTTAATAACCAGTGACATAATTACCGTGCAAGGCACCCTACTGAACACTGGAAAAGATGTTCACGATACGCTGACCTGCGGCAAAATAACCAGGAAAAATCCAGGTATTTCCTCACGTTTTAAg   <  2:61264/139‑1 (MQ=255)                                                                                                                               cccAGGGAAAATTGGTTAATAACCAGTGACATAATTACCGTGCAAGGCACCCTACTGAACACTGGAAAAGATGTTCACGATACGCTGACCTGCGGCAAAATAACCAGGAAAAATCCAGGTATTTCCTCACGTTTTAAGc  <  1:708977/139‑1 (MQ=255)                                                                                                                                     |                                                                                                                                     ATTAACGGAGCTGACCGGTGCCGGTGGATTTGAAGTGTCAGAACAGCCTGCCAGCCATAGCGAAACCAGTGACAAAGCCGCAATGCGGCGAACGGTGAATTTTGGGCTTCCCGCGCTCATTTATCCCCCAGGAAAAATTGGTTAATAACCAGTGACATAATTACCGTGCAAGGCACCCTACTGAACACTGGAAAAGATGTTCACGATACGCTGACCTGCGGCAAAATAACCAGGAAAAATCCAGGTATTTCCTCACGTTTTAAGC  >  NZ_CP009273/2861993‑2862257

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑