Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	1,201,334	T→C	pseudogene (148/408 nt)	BW25113_RS05975 →	phage portal protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,201,334	0	T	C	100.0%	49.2 / NA	16	pseudogene (148/408 nt)	BW25113_RS05975	phage portal protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (12/4);  total (12/4)

GTCGTATGACACCTATACCGGAAAGCAGATCAGCAGTCAGCGGGCTATGCGACTGACGGCGGTTTTTTCCTGCGTCAGAGTGCTGGCAGAGTCGGTCGGGATGTTGCCCTGCAATCTGTATCACCTGAACGGCAGCCTGAAG  >  NZ_CP009273/1201267‑1201408                                                                    |                                                                           gTCGTATGACACCTATACCGGAAAGCAGATCAGCAGTCAGCGGGCTATGCGACTGACGGCGGTTTTTCCCTGCGTCaga                                                                 >  1:190216/1‑79 (MQ=255) gTCGTATGACACCTATACCGGAAAGCAGATCAGCAGTCAGCGGGCTATGCGACTGACGGCGGTTTTTCCCTGCGTCaga                                                                 <  2:190216/79‑1 (MQ=255) gTCGTATGACACCTATACCGGAAAGCAGATCAGCAGTCAGCGGGCTATGCGACTGACGGCGGTTTTTCCCTGCGTCAGAGTGCTGGCaga                                                      >  1:1010556/1‑90 (MQ=255)      aTGACACCTATACCGGAAAGCAGATCAGCAGTCAGCGGGCTATGCGACTGACGGCGGTTTTTCCCTGCGTCAGAGTGCTGGCAGAgtcgg                                                 >  2:436099/1‑90 (MQ=255)              tataCCGGAAAGCAGATCAGCAGTCAGCGGGCTATGCGACTGACGGCGGTTTTTCCCTGCGTCAGAGGGCTGGCAGAGGCGGTCGGGGTg                                         >  2:771010/1‑90 (MQ=255)                    ggAAAGCAGATCAGCAGTCAGCGGGCTATGCGACTGACGGCGGTTTTTCCCTGCGTCAGGGTGTGGGCATAGTCGGTGGGGATGTTGccc                                   >  1:1024443/1‑90 (MQ=255)                    ggAAAGCAGATCAGCAGTCAGCGGGCTATGCGACTGACGGCGGTTTTTCCCTGCGTCAGAGTGCTGGCAGAGTCGGTCGGGATGTTGccc                                   <  1:771010/90‑1 (MQ=255)                     gAAAGCAGATCAGCAGTCATCGGTCTATGCTACTGACGGCGGTTTTTCCCTGCGTCAGAGTGCTGGCAGATTCGGTCGGGATGTTGCCCt                                  >  1:312945/1‑90 (MQ=255)                         gCAGATCAGCAGTCAGCGGGCTATGCGACTGACGGCGGTTTTTCCCTGCGTCAGAGTGCTGGCAGAGTCGGTCGGGATGTTGCCCTGCaa                              <  1:436099/90‑1 (MQ=255)                                      cAGCGGGCTATGCGACTGACGGCGGTTTTTCCCTGCGTCAGAGTGCTGGCAGAGTCGGTCGGGATGTTGCCCTGCAATCTGTATCACCTg                 >  1:434835/1‑90 (MQ=255)                                      cAGCGGGCTATGCGACTGACGGCGGTTTTTCCCTGCGTCAGAGTGCTGGCAGAGTCGGTCGGGATGTTGCCCTGCAATCTGTATCACCTg                 >  1:690299/1‑90 (MQ=255)                                        gCGGGCTATGCGACTGACGGCGGTTTTTCCCTGCGTCAGAGTGCTGGCAGAGTCGGTCGGGATGTTGCCCTGCAATCTGTATCACCTGaa               >  1:501341/1‑90 (MQ=255)                                            tcTATGCTACTGACGGCGGTTTTTCCCTGCGTCAGAGTGCTGGCAGATTCGGTCGGGATGTTGCCCTGCAATCTGTATCACCTGAACGGc           <  2:312945/89‑1 (MQ=255)                                              tATGCGACTGACGGCGGTTTTTCCCTGCGTCAGAGTGCTGGCAGAGTCGGTCGGGATGTTGCCCTGCAATCTGTATCACCTGAACGGCAg         >  1:583448/1‑90 (MQ=255)                                                  cGACTGACGGCGGTTTTTCCCTGGGTCAGAGTGCTGGCAGGGGCGGGCGGGGTGTTGGCCGGCAATCTGGGTCACATGAACGGCGGcccg     >  2:13471/1‑88 (MQ=255)                                                     cTGACGGCGGTTTTTCCCTGCGTCAGAGTGCTGGCAGAGTCGGTCGGGATGTTGCCCTGCAATCTGTATCACCTGAACGGCAGCCTGAAg  >  1:762988/1‑90 (MQ=255)                                                                    |                                                                           GTCGTATGACACCTATACCGGAAAGCAGATCAGCAGTCAGCGGGCTATGCGACTGACGGCGGTTTTTTCCTGCGTCAGAGTGCTGGCAGAGTCGGTCGGGATGTTGCCCTGCAATCTGTATCACCTGAACGGCAGCCTGAAG  >  NZ_CP009273/1201267‑1201408

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑