Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	1,645,059	A→G	pseudogene (725/768 nt)	BW25113_RS23850 →	exonuclease

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,645,059	0	A	G	100.0%	75.5 / NA	22	pseudogene (725/768 nt)	BW25113_RS23850	exonuclease
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (9/13);  total (9/13)

ACCGGAAAATACACGTCTGTTGTTGATCTCGCCCGCGCCAGAGCCAATCAACAGTACACTGAAAATTCAACAGGAAAAATCAGCCCGGTCATTGCTGCCATTCATCGCGAATACAAGCAGACATGGAAAACACTGGATGACGAACTGGCCTATGGGCGCTGCTTCGCAGACAGGCAGAACTTGATGGTATGCCTGCGATCAATGCCAAACGTGTTTACCGGATCATGCGCCAGAATGCGCT  >  NZ_CP009273/1644950‑1645190                                                                                                              |                                                                                                                                    aCCGGAAAATACACGTCTGTTGTTGATCTCGCCCGCGCCAGAGCCAATCAACAGTACACTGAAAATTCAACAGGAAAAATCAGCCCGGTCATTGCTGCCATTCATCGCGGATACAAGCAGACATGGAAAACACTGGATg                                                                                                        <  1:398781/139‑1 (MQ=255)       aaaTACACGTCTGTTGTTGATCTCGCCCGCGCCAGAGCCAATCAACAGTACACTGAAAATTCAACAGGAAAAATCAGCCCGGTCATTGCTGCCATTCATCGCGGATACAAGCAGACATGGAAAACACTGGATGACGAAc                                                                                                  <  1:379836/139‑1 (MQ=255)       aaaTACACGTCTGTTGTTGATCTCGCCCGCGCCAGAGCCAATCAACAGTACACTGAAAATTCAACAGGAAAAATCAGCCCGGTCATTGCTGCCATTCATCGCGGATACAAGCAGACATGGAAAACACTGGATGACGAAc                                                                                                  <  2:211482/139‑1 (MQ=255)             acGTCTGTTGTTGATCTCGCCCGCGCCAGAGCCAATCAACAGTACACTGAAAATTCAACAGGAAAAATCAGCCCGGTCATTGCTGCCATTCATCGCGGATACAAg                                                                                                                              >  2:410807/1‑105 (MQ=255)             acGTCTGTTGTTGATCTCGCCCGCGCCAGAGCCAATCAACAGTACACTGAAAATTCAACAGGAAAAATCAGCCCGGTCATTGCTGCCATTCATCGCGGATACAAg                                                                                                                              <  1:410807/105‑1 (MQ=255)               gTCTGTTGTTGATCTCGCCCGCGCCAGAGCCAATCAACAGTACACTGAAAATTCAACAGGAAAAATCAGCCCGGTCATTGCTGCCATTCATCGCGGATACAAGCAGACATGGAAAACACTGGATGACGAAc                                                                                                  <  2:44450/131‑1 (MQ=255)               gTCTGTTGTTGATCTCGCCCGCGCCAGAGCCAATCAACAGTACACTGAAAATTCAACAGGAAAAATCAGCCCGGTCATTGCTGCCATTCATCGCGGATACAAGCAGACATGGAAAACACTGGATGACGAAc                                                                                                  >  1:44450/1‑131 (MQ=255)                  tgttgtTGATCTCGCCCGCGCCAGAGCCAATCAACAGTACACTGAAAATTCAACAGGAAAAATCAGCCCGGTCATTGCTGCCATTCATCGCGGATACa                                                                                                                                <  2:576020/98‑1 (MQ=255)                  tgttgtTGATCTCGCCCGCGCCAGAGCCAATCAACAGTACACTGAAAATTCAACAGGAAAAATCAGCCCGGTCATTGCTGCCATTCATCGCGGATACa                                                                                                                                >  1:576020/1‑98 (MQ=255)                          aTCTCGCCCGCGCCAGAGCCAATCAACAGCACACTGAAAATTCAACAGGAAAAATCAGCCCGGTCATTGCTGCCATTCATCGCGGATACAAGCAGACATGGAAAACACTGGATGACGAACTGGCCTATGGGCGCTGCtt                                                                               >  1:141241/1‑139 (MQ=255)                               gCCCGCGCCAGAGCCAATCAACAGTACACTGAAAATTCAACAGGAAAAATCAGCCCGGTCATTGCTGCCATTCATCGCGGATACAAGCAGACATGGAAAACACTGGATGACGAACTGGCCTATGGGCGCTGCTTCGCAg                                                                          <  1:366167/139‑1 (MQ=255)                                cccGCGCCAGAGCCAATCAACAGTACACTGAAAATTCAACAGGAAAAATCAGCCCGGTCATTGCTGCCATTCATCGCGGATACAAGCAGACATGGAAAACACTGGATGACGAACTGGCCTATGGGCGCTGCTTCGCAGa                                                                         <  1:110395/139‑1 (MQ=255)                                               aTCAACAGTACACTGAAAATTCAACAGGAAAAATCAGCCCGGTCATTGCTGCCATTCATCGCGGATACAAGCAGACATGGAAAACACTGGATGACGAACTGGCCTATGGGCGCTGCTTCGCAGa                                                                         <  2:1965/124‑1 (MQ=255)                                               aTCAACAGTACACTGAAAATTCAACAGGAAAAATCAGCCCGGTCATTGCTGCCATTCATCGCGGATACAAGCAGACATGGAAAACACTGGATGACGAACTGGCCTATGGGCGCTGCTTCGCAGa                                                                         >  1:1965/1‑124 (MQ=255)                                                      gTACACTGAAAATTCAACAGGAAAAATCAGCCCGGTCATTGCTGCCATTCATCGCGGATACAAGCAGACATGGAAAACACTGGATGACGAACTGGCCTATGGGCGCTGCTTCGCAGACAGGCAGAACTTGATGGTATGc                                                   >  2:47074/1‑139 (MQ=255)                                                         cacTGAAAATTCAACAGGAAAAATCAGCCCGGTCATTGCTGCCATTCATCGCGGATACAAGCAGACATGGAAAACACTGGATGACGAACTGGCCTATGGGCGCTGCTTCGCAGACAGGCAGAACTTGATGGTATGCCTg                                                >  1:61095/1‑139 (MQ=255)                                                              aaaaTTCAACAGGAAAAATCAGCCCGGTCATTGCTGCCATTCATCGCGGATACAAGCAGGCATGGAAAACACTGGATGACGAACTGGCCTTTGGGCGCTGCTTCGCAGACAGGCAGAACTTGATGGTATGCCTGCGAt                                            <  2:244977/138‑1 (MQ=255)                                                                          gAAAAATCAGCCCGGTCATTGCTGCCATTCATCGCGGATACAAGCAGACATGGAAAACACTGGATGACGAACTGGCCTATGGGCGCTGCTTCGCAGACAGGCAGAACTTGATGGTATGCCTGCGATCAATGCCAAACgt                               <  1:544096/139‑1 (MQ=255)                                                                                      cGGTCATTGCTGCCATTCATCGCGGATACAAGCAGACATGGAAAACACTGGATGACGAACTGGCCTATGGGCGCTGCTTCGCAGACAGGCAGAACTTGATGGTATGCCTGCGATCAATGCCAAACGTGTTTACCGGATc                   <  2:424408/139‑1 (MQ=255)                                                                                             tgctgcCATTCATCGCGGATACAAGCAGACATGGAAAACACTGGATGACGAACTGGCCTATGGGCGCTGCTTCGCAGACAGGCAGAACTTGATGGTATGCCTGCGATCAATGCCa                                    <  1:471562/115‑1 (MQ=255)                                                                                             tgctgcCATTCATCGCGGATACAAGCAGACATGGAAAACACTGGATGACGAACTGGCCTATGGGCGCTGCTTCGCAGACAGGCAGAACTTGATGGTATGCCTGCGATCAATGCCa                                    >  2:471562/1‑115 (MQ=255)                                                                                                       cATCGCGGATACAAGCAGACATGGAAAACACTGGATGACGAACTGGCCTATGGGCGCTGCTTCGCAGACAGGCAGAACTTGATGGTATGCCTGCGATCAATGCCAAACGTGTTTACCGGATCATGCGCCAGAATGCGCt  >  2:50405/1‑139 (MQ=255)                                                                                                              |                                                                                                                                    ACCGGAAAATACACGTCTGTTGTTGATCTCGCCCGCGCCAGAGCCAATCAACAGTACACTGAAAATTCAACAGGAAAAATCAGCCCGGTCATTGCTGCCATTCATCGCGAATACAAGCAGACATGGAAAACACTGGATGACGAACTGGCCTATGGGCGCTGCTTCGCAGACAGGCAGAACTTGATGGTATGCCTGCGATCAATGCCAAACGTGTTTACCGGATCATGCGCCAGAATGCGCT  >  NZ_CP009273/1644950‑1645190

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑