Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	1,200,135	(A)5→4	pseudogene (279/1137 nt)	BW25113_RS05965 →	terminase large subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,200,131	0	A	.	100.0%	155.4 / NA	35	pseudogene (275/1137 nt)	BW25113_RS05965	terminase large subunit
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base . (25/10);  total (25/10)

ACGGCTCGGTGCCAAACGATGAACTGTTCGGGATCATCTATACCGTTGATGAAGGTGACGACTGGACCGACCCGCAGGTGCTGGAAAAAGCCAATCCAAATATTGGCGTGTCGGTTTATCGCGAATTTTTGTTAAGTCAGCAGCAGCGTGCGAAAAATAACGCCCGTCTGG  >  NZ_CP009273/1200047‑1200217                                                                                     |                                                                                       aCGGCTCGGTGCCAAACGATGAACTGTTCGGGATCATCTATACCGTTGATGAAGGTGACGACTGGACCGACCCGCAGGTGCTGGaaaagcc                                                                                  <  2:202375/91‑4 (MQ=255) aCGGCTCGGTGCCAAACGATGAACTGTTCGGGATCATCTATACCGTTGATGAAGGTGACGACTGGACCGACCCGCAGGTGCTGGaaaagcc                                                                                  <  2:568895/91‑4 (MQ=255)      tCGGTGCCAAACGATGAACTGTTCGGGATCATCTATACCGTTGATGAAGGTGACGACTGGACCGACCCGCAGGTGCTGG‑AAAAGCCAATcc                                                                            >  1:58282/1‑91 (MQ=255)       cGGTGCCAAACGATGAACTGTTCGGGATCATCTATACCGTTGATGAAGGTGACGACTGGACCGACCCGCAGGTGCTGG‑AAAAGCCAATCCa                                                                           <  1:284773/91‑1 (MQ=255)       cGGTGCCAAACGATGAACTGTTCGGGATCATCTATACCGTTGATGAAGGTGACGACTGGACCGACCCGCAGGGGCTGG‑AAAAGCCAAACCa                                                                           >  2:733224/1‑91 (MQ=255)                     gAACTGTTCGGGATCATCTATACCGTTGATGAAGGTGACGACTGGACCGACCCGCAGGTGCTGG‑AAAAGCCAATCCAAATATTGGCGTGTc                                                             >  1:492457/1‑91 (MQ=255)                            tCGGGATCATCTATACCGTTGATGAAGGTGACGACTGGACCGACCCGCAGGTGCTGG‑AAAAGCCAATCCAAATATTGGCGTGTCGGTTTAt                                                      >  1:828975/1‑91 (MQ=255)                                    atcTATACCGTTGATGAAGGTGACGACTGGACCGACCCGCCGGCGCCGG‑AAAAGCCAATCCAAATATTGGCGTGTCGGGTTATCGCGCAtt                                              >  2:484166/1‑91 (MQ=255)                                    atcTATACCGTTGATGAAGGTGACGACTGGACCGACCCGCAGGTGCTGG‑AAAAGCCAATCCa                                                                           >  1:335504/1‑62 (MQ=255)                                    atcTATACCGTTGATGAAGGTGACGACTGGACCGACCCGCAGGTGCTGG‑AAAAGCCAATCCa                                                                           <  2:335504/62‑1 (MQ=255)                                    atcTATACCGTTGATGAAGGTGACGACTGGACCGACCCGCAGGTGCTGG‑AAAAGCCAATCCAAATATTGGCGTGTCGGTTTATCGCGAAtt                                              >  1:443674/1‑91 (MQ=255)                                    atcTATACCGTTGATGAAGGTGACGACTGGACCGACCCGCAGGTGCTGG‑AAAAGCCAATCCAAATATTGGCGTGTCGGTTTATCGCGAAtt                                              >  2:744123/1‑91 (MQ=255)                                          aCCGTTGATGAAGGTGACGACTGGACCGACCCGCAGGTGCTGG‑AAAAGCCAATCCAAATATTGGCGTGTCGGTTTATCGCGAATTTTTGtt                                        <  1:179010/91‑1 (MQ=255)                                             gTTGATGAAGGTGACGACTGGACCGCCCCGCAGGTGCTGG‑AAAAGCCAATCCAAATATTGGCGTGTCGGTTTATCGCGAATTTTTGTTAAg                                     >  2:413889/1‑91 (MQ=255)                                             gTTGATGAAGGTGACGACTGGACCGACCCGCAGGTGCTGG‑AAAAGCCAATCCAAATATTGGCGTGTCGGTTTATCGCGAATTTTTGTTAAg                                     >  1:824589/1‑91 (MQ=255)                                             gTTGATGAAGGTGACGACTGGACCGACCCGCAGGTGCTGG‑AAAAGCCAATCCAAATATTGGCGTGTCGGTTTATCGCGAATTTTTGTTAAg                                     <  2:177655/91‑1 (MQ=255)                                             gTTGATGAAGGTGACGACTGGACCGACCCGCAGGTGCTGG‑AAAAGCCAATCCAAATATTGGCGTGTCGGTTTATCGCGAATTTTTGTTAAg                                     >  1:125728/1‑91 (MQ=255)                                             gTTGATGAAGGTGACGACTGGACCGACCCGCAGGTGCTGG‑AAAAGCCAATCCAAATATTGGCGTGTCGGTTTATCGCGAATTTTTGTTAAg                                     <  2:238638/91‑1 (MQ=255)                                             gTTGATGAAGGTGACGACTGGACCGACCCGCAGGTGCTGG‑AAAAGCCAATCCAAATATTGGCGTGTCGGTTTATCGCGAATTTTTGTTAAg                                     >  2:44146/1‑91 (MQ=255)                                             gTTGATGAAGGTGACGACTGGACCGACCCGCAGGTGCTGG‑AAAAGCCAATCCAAATATTGGCGTGTCGGTTTATCGCGAATTTTTGTTAAg                                     <  2:683347/91‑1 (MQ=255)                                             gTTGATGAAGGTGACGACTGGACCGACCCGCAGGTGCTGG‑AAAAGCCAATCCAAATATTGGCGTGTCGGTTTATCGCGAATTTTTGTTAAg                                     >  1:612410/1‑91 (MQ=255)                                             gTTGATGAAGGTGACGACTGGACCGACCCGCAGGTGCTGG‑AAAAGCCAATCCAAATATTGGCGTGTCGGTTTATCGCGAATTTTTGTTAAg                                     >  1:463959/1‑91 (MQ=255)                                             gTTGATGAAGGTGACGACTGGACCGACCCGCAGGTGCTGG‑AAAAGCCAATCCAAATATTGGCGTGTCGGTTTATCGCGAATTTTTGTTAAg                                     >  1:238638/1‑91 (MQ=255)                                             gTTGATGAAGGTGACGACTGGACCGACCCGCAGGTGCTGG‑AAAAGCCAATCCAAATATTGGCGTGTCGGTTTATCGCGAATTTTTGTTAAg                                     <  1:195818/91‑1 (MQ=255)                                              ttGATGAAGGTGACGACTGGACCGACCCGCAGGTGCTGG‑AAAAGCCAATCCAAATATTGGCGTGTCGGTTTATCGCGAATTTTTGTTAAGt                                    >  1:812808/1‑91 (MQ=255)                                               tgatgaAGGTGACGACTGGACCGACCCGCAGGTGCTGG‑AAAAGCCAATCCAAATATTGGCGTGTCGGTTTATCGCGAATTTTTGTTAAGTc                                   >  1:713333/1‑91 (MQ=255)                                               tgatgaAGGTGACGACTGGACCGACCCGCAGGTGCTGG‑AAAAGCCAATCCAAATATTGGCGTGTCGGTTTATCGCGAATTTTTGTTAAGTc                                   >  2:177339/1‑91 (MQ=255)                                               tgatgaAGGTGACGACTGGACCGACCCGCAGGTGCTGG‑AAAAGCCAATCCAAATATTGGCGTGTCGGTTTATCGCGAATTTTTGTTAAGTc                                   >  1:684216/1‑91 (MQ=255)                                                  tgaAGGTGACGACTGGACCGACCCGCAGGTGCTGG‑AAAAGCCAATCCAAATATTGGCGTGTCGGTTTATCGCGAATTTTTGTTAAGTcagc                                >  2:170538/1‑91 (MQ=255)                                                                ggACCGACCCGCAGGTGCTGG‑AAAAGCCAATCCAAATATTGGCGTGTCGGTTTATCGCGAATTTTTGTTAAGTCAGCAGCAGCGTGCGaaa                  >  1:465954/1‑91 (MQ=255)                                                                ggACCGACCCGCAGGTGCTGG‑AAAAGCCAATCCAAATATTGGCGTGTCGGTTTATCGCGAATTTTTGTTAAGTCAGCAGCAGCGTGCGaaa                  >  2:365696/1‑91 (MQ=255)                                                                     gaccCGCAGGTGCTGG‑AAAAGCCAATCCAAATATTGGCGTGTCGGTTTATCGCGAATTTTTGTTAAGTCAGCAGCAGCGTGCGAAAAATaa             >  1:690675/1‑91 (MQ=255)                                                                     gaccCGCAGGTGCTGG‑AAAAGCCAATCCAAATATTGGCGTGTCGGTTTATCGCGAATTTTTGTTAAGTCAGCAGCAGCGTGCGAAAAATaa             >  2:400563/1‑91 (MQ=255)                                                                      accCGCAGGTGCTGG‑AAAAGCCAATCCAAATATTGGCGTGTCGGTTTATCGCGAATTTTTGTTAAGTCAGCAGCAGCGTGCGAAAAATAAc            <  1:400563/91‑1 (MQ=255)                                                                         cGCAGGTGCTGG‑AAAAGCCAATCCAAATATTGGCGTGTCGGTTTATCGCGAATTTTTGTTAAGTCAGCAGCAGCGTGCGAAAAATAACGcc         <  2:824589/91‑1 (MQ=255)                                                                             ggTGCTGG‑AAAAGCCAATCCAAATATTGGCGTGTCGGTTTATCGCGAATTTTTGTTAAGTCAGCAGCAGCGTGCGAAAAATAACGCCCGTc     <  1:177339/91‑1 (MQ=255)                                                                               tGCTGG‑AAAAGCCAATCCAAATATTGGCGTGTCGGTTTATCGCGAATTTTTGTTAAGTCAGCAGCAGCGTGCGAAAAATAACGCCCGTCTg   >  1:592759/1‑91 (MQ=255)                                                                                gCTGG‑AAAAGCCAATCCAAATATTGGCGTGTCGGTTTATCGCGAATTTTTGTTAAGTCAGCAGCAGCGTGCGAAAAATAACGCCCGTCTgg  >  1:602468/1‑91 (MQ=255)                                                                                     |                                                                                       ACGGCTCGGTGCCAAACGATGAACTGTTCGGGATCATCTATACCGTTGATGAAGGTGACGACTGGACCGACCCGCAGGTGCTGGAAAAAGCCAATCCAAATATTGGCGTGTCGGTTTATCGCGAATTTTTGTTAAGTCAGCAGCAGCGTGCGAAAAATAACGCCCGTCTGG  >  NZ_CP009273/1200047‑1200217

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑