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%	58.2 / NA	17	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 (5/12);  total (5/12)

AGCTGACCGGTGCCGGTGGATTTGAAGTGTCAGAACAGCCTGCCAGCCATAGCGAAACCAGTGACAAAGCCGCAATGCGGCGAACGGTGAATTTTGGGCTTCCCGCGCTCATTTATCCCCCAGGAAAAATTGGTTAATAACCAGTGACATAATTACCGTGCAAGGCACCCTACTGAACACTGGAAAAGATGTTCACGATACGCTGACCTGCGGCAAAATAACCAGG  >  NZ_CP009273/2862001‑2862226                                                                                                                             |                                                                                                      aGCTGACCGGTGCCGGTGGATTTGAAGTGTCAGAACAGCCTGCCAGCCATAGCGAAACCAGTGACAAAGCCGCAATGCGGCGAACGGTGAATTTTGGGCTTCCCGCGCTCATTTATCCCCCAGGGAAAATTGGTtaat                                                                                          >  2:12458/1‑138 (MQ=255)      aCCGGTGCCGGTGGATTTGAAGTGTCAGAACAGCCTGCCAGCCATAGCGAAACCAGTGACAAAGCCGCAATGCGGCGAACGGTGAATTTTGGGCTTCCCGCGCTCATTTATCCCCCAGGGAAAATTGGTTAATAACCAg                                                                                    >  2:528103/1‑139 (MQ=255)       ccggtgccggtgGATTTGAAGTGTCAGAACAGCCTGCCAGCCATAGCGAAACCAGTGACAAAGCCGCAATGCGGCGAACGGTGAATTTTGGGCTTCCCGCGCTCATTTATCCCCCAGGGAAAATTGGTTAATAACCAGt                                                                                   <  1:12458/139‑1 (MQ=255)       ccggtgccggtgGATTTGAAGTGTCAGAACAGCCTGCCAGCCATAGCGAAACCAGTGACAAAGCCGCAATGCGGCGAACGGTGAATTTTGGGCTTCCCGCGCTCATTTATCCCCCAGGGAAAATTGGTTAATAACCAGt                                                                                   <  2:12886/139‑1 (MQ=255)       ccggtgccggtgGATTTGAAGTGTCAGAACAGCCTGCCAGCCATAGCGAAACCAGTGACAAAGCCGCAATGCGGCGAACGGTGAATTTTGGGCTTCCCGCGCTCATGTATCCCCCAGGGAAAATTGGTTAATAACCAGt                                                                                   <  1:506382/139‑1 (MQ=255)           tgccggtgGATTTGAAGTGTCAGAACAGCCTGCCAGCCATAGCGAAACCAGTGACAAAGCCGCAATGCGGCGAACGGTGAATTTTGGGCTTCCCGCGCTCATTTATCCCCCAGGGAAAATTGGTTAATAACCAGTGACa                                                                               >  1:529028/1‑139 (MQ=255)                              tCAGAACAGCCTGCCAGCCATAGCGAAACCAGTGACAAAGCCGCAATGCGGCGAACGGTGAATTTTGGGCTTCCCGCGCTCATTTATCCCCCAGGGAAAATTGGTTAATAACCAGTGACATAATTACCGTGCAAGGCa                                                             <  1:453247/138‑1 (MQ=255)                              tCAGAACAGCCTGCCAGCCATAGCGAAACCAGTGACAAAGCCGCAATGCGGCGAACGGTGAATTTTGGGCTTCCCGCGCTCATTTATCCCCCAGGGAAAATTGGTTAATAACCAGTGACATAATTACCGTGCAAGGCa                                                             <  1:158712/138‑1 (MQ=255)                              tCAGAACAGCCTGCCAGCCATAGCGAAACCAGTGACAAAGCCGCAATGCGGCGAACGGTGAATTTTGGGCTTCCCGCGCTCATTTATCCCCCAGGGAAAATTGGTTAATAACCAGTGACATAATTACCGTGCAAGGCa                                                             <  2:359515/138‑1 (MQ=255)                              tCAGAACAGCCTGCCAGCCATAGCGAAACCAGTGACAAAGCCGCAATGCGGCGAACGGTGAATTTTGGGCTTCCCGCGCTCATTTATCCCCCAGGGAAAATTGGTTAATAACCAGTGACATAATTACCGTGCAAGGCAc                                                            >  1:359881/1‑139 (MQ=255)                                aGAACAGCCTGCCAGCCATAGCGAAACCAGTGACAAAGCCGCAATGCGGCGAACGGTGAATTTTGGGCTTCCCGCGCTCATTTATCCCCCAGGGAAAATTGGTTAATAACCAGTGACATAATTACCGTGCAAGGCAcc                                                           <  2:154640/138‑1 (MQ=255)                                        cTGCCAGCCATAGCGAAACCAGTGACAAAGCCGCAATGCGGCGAACGGTGAATTTTGGGCTTCCCGCGCTCATTTATCCCCCAGGGAAAATTGGTTAATAACCAGTGACATAATTACCGTGCAAGGCACCCTACTGaa                                                   >  2:381805/1‑138 (MQ=255)                                                          ccAGTGACAAAGCCGCAATGCGGCGAACGGTGAATTTTGGGCTTCCCGCGCTCATTTATCCCCCAGGGAAAATTGGTTAATAACCAGTGACATAATTACCGTGCAAGGCACCCTACTGAACACTGGAAAAGATGTTCAc                                <  1:118665/139‑1 (MQ=255)                                                           cAGTGACAAAGCCGCAATGCGGCGAACGGTGAATTTTGGGCTTCCCGCGCTCATTTATCCCCCAGGGAAAATTGGTTAATAACCAGTGACATAATTACCGTGCAAGGCACCCTACTGAACACTGGAAAAGATGTTCACg                               <  2:529028/139‑1 (MQ=255)                                                                                    aCGGTGAATTTTGGGCTTCCCGCGCTCATTTATCCCCCAGGGAAAATTGGTTAATAACCAGTGACATAATTACCGTGCAAGGCACCCTACTGAACACTGGAAAAGATGTTCACGATACGCTGACCTGCGGCAAAATAAc      <  1:381805/139‑1 (MQ=255)                                                                                     cGGTGAATTTTGGGCTTCCCGCGCTCATTTATCCCCCAGGGAAAATTGGTTAATAACCAGTGACATAATTACCGTGCAAGGCACCCTACTGAACACTGGAAAAGATGTTCACGATACGCTGACCTGCGGCAAAATAAcc     <  2:359881/139‑1 (MQ=255)                                                                                        tGAATTTTGGGCTTCCCGCGCTCATTTATCCCCCAGGgaaaa                                                                                                   >  2:557532/1‑42 (MQ=255)                                                                                        tGAATTTTGGGCTTCCCGCGCTCATTTATCCCCCAGGgaaaa                                                                                                   <  1:557532/42‑1 (MQ=255)                                                                                        tGAATTTTGGGCTTCCCGCGCTCATTTATCCCCCAGGGAAAATTGGTTAATAACCAGTGACATAATGACCGTGCAAGGCGCCCTACTGAACACGGGAAAAGATGTTCACGAGACGCTGTCCTGCGGCAAAATAACCAgg  <  1:134769/139‑1 (MQ=255)                                                                                                                             |                                                                                                      AGCTGACCGGTGCCGGTGGATTTGAAGTGTCAGAACAGCCTGCCAGCCATAGCGAAACCAGTGACAAAGCCGCAATGCGGCGAACGGTGAATTTTGGGCTTCCCGCGCTCATTTATCCCCCAGGAAAAATTGGTTAATAACCAGTGACATAATTACCGTGCAAGGCACCCTACTGAACACTGGAAAAGATGTTCACGATACGCTGACCTGCGGCAAAATAACCAGG  >  NZ_CP009273/2862001‑2862226

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑