Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	1,645,076	A→G	pseudogene (742/768 nt)	BW25113_RS23850 →	exonuclease

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,645,076	0	A	G	100.0%	96.7 / NA	25	pseudogene (742/768 nt)	BW25113_RS23850	exonuclease
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (16/9);  total (16/9)

GGAAACCGGAAAATACACGTCTGTTGTTGATCTCGCCCGCGCCAGAGCCAATCAACAGTACACTGAAAATTCAACAGGAAAAATCAGCCCGGTCATTGCTGCCATTCATCGCGAATACAAGCAGACATGGAAAACACTGGATGACGAACTGGCCTATGGGCGCTGCTTCGCAGACAGGCAGAACTTGATGGTATGCCTGCGATCAATGCCAAACGTGTTTACCGGATCATGCGCCAGAATGCGCTGTTGCTTGAGCGAAAACC  >  NZ_CP009273/1644946‑1645208                                                                                                                                   |                                                                                                                                     ggAAACCGGAAAATACACGTCTGTTGTTGATCTCGCCCGCGCCAGAGCCAATCAACAGTACACTGAAAATTCAACAGGAAAAATCAGCCCGGTCATTGCTGCCATTCATCGCGAATACAAGCAGACATGGGAAACACTg                                                                                                                              >  2:607748/1‑139 (MQ=255)                              aTCTCGCCCGCGCCAGAGCCAATCAACAGTACACTGAAAATTCAACAGGAAAAATCAGCCCGGTCATTGCTGCCATTCATCGCGAATACAAGCAGACATGGGAAACACTGGATGACGAACTGGCCTATGGgcg                                                                                                       <  2:637032/133‑1 (MQ=255)                              aTCTCGCCCGCGCCAGAGCCAATCAACAGTACACTGAAAATTCAACAGGAAAAATCAGCCCGGTCATTGCTGCCATTCATCGCGAATACAAGCAGACATGGGAAACACTGGATGACGAACTGGCCTATGGgcg                                                                                                       >  1:637032/1‑133 (MQ=255)                                        cgcCAGAGCCAATCAACAGTACACTGAAAATTCAACAGGAAAAATCAGCCCGGTCATTGCTGCCATTCATCGCGAATACAAGCAGACATGGGAAACACTGGATGACGAACTGGCCTATGGGCGCTGCTTCGCAGACAgg                                                                                       >  1:352985/1‑139 (MQ=255)                                          ccAGAGCCAATCAACAGTACACTGAAAATTCAACAGGAAAAATCAGCCCGGTCATTGCTGCCATTCATCGCGAATACAAGCAGACATGGGAAACACTGGATGACGAACTGGCCTATGGGCGCTGCTTCGCAGACAGGCa                                                                                     <  2:352985/139‑1 (MQ=255)                                                   aTCAACAGTACACTGAAAATTCAACAGGAAAAATCAGCCCGGTCATTGCTGCCATTCATCGCGAATACAAGCAGACATGGGAAACACTGGATGACGAACTGGCCTATGGGCGCTGCTTCGCAGACAGGCAGAACTTGAt                                                                            >  1:430608/1‑139 (MQ=255)                                                   aTCAACAGTACACTGAAAATTCAACAGGAAAAATCAGCCCGGTCATTGCTGCCATTCATCGCGAATACAAGCAGACATGGGAAACACTGGATGACGAACTGGCCTATGGGCGCTGCTTCGCAGACAGGCAGAACTTGAt                                                                            >  1:522127/1‑139 (MQ=255)                                                           tACACTGAAAATTCAACAGGAAAAATCAGCCCGGTCATTGCTGCCATTCATCGCGAATACAAGCAGACATGGGAAACACTGGATGACGAACTGGCCTATGGGCGCTGCTTCGCAGACAGGCAGAACTTGATGGTATGcc                                                                    >  2:54460/1‑139 (MQ=255)                                                             cacTGAAAATTCAACAGGAAAAATCAGCCCGGTCATTGCTGCCATTCATCGCGAATACAAGCAGACATGGGAAACACTGGATGACGAACTGGCCTATGGGCGCTGCTTCGCAGACAGGCAGAACTTGATGGTATGCCTg                                                                  >  1:356596/1‑139 (MQ=255)                                                             cacTGAAAATTCAACAGGAAAAATCAGCCCGGTCATTGCTGCCATTCATCGCGAATACAAGCAGACATGGGAAACACTGGATGACGAACTGGCCTATGGGCGCTGCTTCGCAGACAGGCAGAACTTGATGGTATGCCTg                                                                  >  2:556869/1‑139 (MQ=255)                                                                  aaaaTTCAACAGGAAAAATCAGCCCGGTCATTGCTGCCATTCATCGCGAATACAAGCAGACATGGGAAACACTGGATGACGAACTGGCCTATGGGCGCTGCTTCGCAGACAGGCAGAACTTGATGGTATGCCTGCGAt                                                              >  2:392398/1‑138 (MQ=255)                                                                  aaaaTTCAACAGGAAAAATCAGCCCGGTCATTGCTGCCATTCATCGCGAATACAAGCAGACATGGGAAACACTGGATGACGAACTGGCCTATGGGCGCTGCTTCGCAGACAGGCAGAACTTGATGGTATGCCTGCGAt                                                              >  2:554011/1‑138 (MQ=255)                                                                       tCAACAGGAAAAATCAGCCCGGTCATTGCTGCCATTCATCGCGAATACAAGCAGACATGGGAAACACTGGATGACGAACTGGCCTAt                                                                                                            <  1:53466/87‑1 (MQ=255)                                                                       tCAACAGGAAAAATCAGCCCGGTCATTGCTGCCATTCATCGCGAATACAAGCAGACATGGGAAACACTGGATGACGAACTGGCCTAt                                                                                                            >  2:53466/1‑87 (MQ=255)                                                                         aaCAGGAAAAATCAGCCCGGTCATTGCTGCCATTCATCGCGAATACAAGCAGACATGGGAAACACTGGATGACGAACTGGCCTATGGGCGCTGCTTCGCAGACAGGCAGAACTTGATGGTATGCCTGCGATCAATGCCa                                                      <  1:556869/139‑1 (MQ=255)                                                                         aaCAGGAAAAATCAGCCCGGTCATTGCTGCCATTCATCGCGAATACAAGCAGACATGGGAAACACTGGATGACGAACTGGCCTATGGGCGCTGCTTCGCAGACAGGCAGAACTTGATGGTATGCCTGCGATCAATGCCa                                                      <  2:430608/139‑1 (MQ=255)                                                                          aCAGGAAAAATCAGCCCGGTCATTGCTGCCATTCATCGCGAATACAAGCAGACATGGGAAACACTGGATGACGAACTGGCCTATGGGCGCTGCTTCGCAGACAGGCAGAACTTGATGGTATGCCTGCGATCAATGCCa                                                      >  1:88443/1‑138 (MQ=255)                                                                            aGGAAAAATCAGCCCGGTCATTGCTGCCATTCATCGCGAATACAAGCAGACATGGGAAACACTGGATGACGAACTGGCCTATGGGCGCTGCTTCGCAGACAGGCAGAACTTGATGGTATGCCTGCGATCAATGCCAAAc                                                   <  2:88443/139‑1 (MQ=255)                                                                                        cccGGTCATTGCTGCCATTCATCGCGAATACAAGCAGACATGGGAAACACTGGATGACGAACTGGCCTATGGGCGCTGCTTCGCAGACAGGCAGAACTTGATGGTATGCCTGCGATCAATGCCAAACGTGttt                                             >  1:209382/1‑133 (MQ=255)                                                                                        cccGGTCATTGCTGCCATTCATCGCGAATACAAGCAGACATGGGAAACACTGGATGACGAACTGGCCTATGGGCGCTGCTTCGCAGACAGGCAGAACTTGATGGTATGCCTGCGATCAATGCCAAACGTGttt                                             <  2:209382/133‑1 (MQ=255)                                                                                                      ccATTCATCGCGAATACAAGCAGACATGGGAAACACTGGATGACGAACTGGCCTATGGGCGCTGCTTCGCAGACAGGCAGAACTTGATGGTATGCCTGCGATCAATGCCAAACGTGTTTACCGGATCATGCGCCAGAAt                         >  1:386472/1‑139 (MQ=255)                                                                                                                  aaTACAAGCAGACATGGGAAACTCTGGATGACGAACTGGCCTATGGGCGCTGCTTCGCAGACAGGCAGAACTTGATGGTATGCCTGCGATCAATGCCAAACGTGTTTACCGGATCATGCGCCAGAATGCGCTGTTGCtt             <  2:499807/139‑1 (MQ=255)                                                                                                                          cAGACATGGGAAACACTGGATGACGAACTGGCCTATGGGCGCTGCTTCGCAGACAGGCAGAACTTGATGGTATGCCTGCGATCAATGCCAAACGTGTTTACCGGATCATGCGCCAGAATGCGCTGTTGCTTGAGCGaaa     <  1:9467/139‑1 (MQ=255)                                                                                                                             aCATGGGAAACACTGGATGACGAACTGGCCTATGGGCGCTGCTTCGCAGACAGGCAGAACTTGATGGTATGCCTGCGATCAATGCCAAACGTGTTTACCGGATCATGCGCCAGAATGCGCTGTTGCTTGAGCGAAAAcc  >  2:46195/1‑139 (MQ=255)                                                                                                                             aCATGGGAAACACTGGATGACGAACTGGCCTATGGGCGCTGCTTCGCAGACAGGCAGAACTTGATGGTATGCCTGCGATCAATGCCAAACGTGTTTACCGGATCATGCGCCAGAATGCGCTGTTGCTTGAGCGAAAAcc  >  2:600957/1‑139 (MQ=255)                                                                                                                                   |                                                                                                                                     GGAAACCGGAAAATACACGTCTGTTGTTGATCTCGCCCGCGCCAGAGCCAATCAACAGTACACTGAAAATTCAACAGGAAAAATCAGCCCGGTCATTGCTGCCATTCATCGCGAATACAAGCAGACATGGAAAACACTGGATGACGAACTGGCCTATGGGCGCTGCTTCGCAGACAGGCAGAACTTGATGGTATGCCTGCGATCAATGCCAAACGTGTTTACCGGATCATGCGCCAGAATGCGCTGTTGCTTGAGCGAAAACC  >  NZ_CP009273/1644946‑1645208

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑