Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	386,045	T→C	pseudogene (339/1527 nt)	BW25113_RS01915 →	outer membrane autotransporter barrel domain‑containing protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	386,045	0	T	C	100.0%	101.0 / NA	32	pseudogene (339/1527 nt)	BW25113_RS01915	outer membrane autotransporter barrel domain‑containing protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (16/16);  total (16/16)

CACGATCTCAACCTATTATTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGTTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATCTGGGTGGATATGATTTTTAC  >  NZ_CP009273/385961‑386126                                                                                     |                                                                                  cACGATCTCAACCTATTATTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGAt                                                                              >  1:115342/1‑90 (MQ=255)  aCGATCTCAACCTATTATTTGAACCATGATTATGCAGGCAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGAtt                                                                             <  1:136220/90‑1 (MQ=255)  aCGATCTCAACCTATTATTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGAtt                                                                             <  1:156968/90‑1 (MQ=255)  aCGATCTCAACCTATTATTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGAtt                                                                             <  1:321811/90‑1 (MQ=255)  aCGATCTCAACCTATTATTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGAtt                                                                             <  1:334522/90‑1 (MQ=255)              tattatTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTAtgctg                                                                 >  1:89380/1‑90 (MQ=255)               attattTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTAtgctgc                                                                >  2:260248/1‑90 (MQ=255)               attattTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTAtgctgc                                                                >  2:44408/1‑90 (MQ=255)               attattTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTAtgctgc                                                                >  2:12380/1‑90 (MQ=255)                    ttGAACCATGATTATGCAGACAGTACTGCAAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGc                                                           <  1:406771/90‑1 (MQ=255)                      gAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCgg                                                         >  1:218691/1‑90 (MQ=255)                                 aTGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATc                                              <  1:433858/90‑1 (MQ=255)                                     aGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGttt                                          >  2:435459/1‑90 (MQ=255)                                      gACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGGTATTATGATCGtttt                                         >  1:462072/1‑90 (MQ=255)                                      gACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCCATTACGTCTATGCTGCCTGGCGGTTTTTATGATCGtttt                                         >  2:194021/1‑90 (MQ=255)                                          gTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTTTGCCGCCTGGCGGTTATTATGGTCGTTTTGAtt                                     >  2:300751/1‑89 (MQ=255)                                               gCTAATCAGCTTGATATCAGTAGTTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGAt                                <  2:362105/90‑1 (MQ=255)                                               gCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGAt                                <  1:308208/90‑1 (MQ=255)                                               gCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGAt                                <  1:143439/90‑1 (MQ=255)                                                    tCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGAtt                                                                             >  1:275480/1‑40 (MQ=39)                                                    tCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGAtt                                                                             <  2:275480/40‑1 (MQ=39)                                                    tCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGAt                                <  1:443705/85‑1 (MQ=255)                                                    tCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGAt                                >  2:443705/1‑85 (MQ=255)                                                    tCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGtaa                           <  1:417945/90‑1 (MQ=255)                                                    tCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTAATTATGATCGTTTTGATGCAGATGGtaa                           >  1:81180/1‑90 (MQ=255)                                                       gCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGtaataa                        >  1:252477/1‑90 (MQ=255)                                                              atCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATCTGGGt                 <  2:313560/90‑1 (MQ=255)                                                                 aGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATCTGGGTGGa              >  2:324742/1‑90 (MQ=255)                                                                     aTTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATCTGGGTGGATATg          <  2:218691/90‑1 (MQ=255)                                                                     aTTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATCTGGGTGGATATg          <  2:470202/90‑1 (MQ=255)                                                                     aTTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGGTATTATGATCGTTTTGATGCAGATGGTAATAATCTGGGTGGATATg          >  1:297248/1‑90 (MQ=255)                                                                             aTTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATCTGGGTGGATATGATTTTTac  <  2:229958/90‑1 (MQ=255)                                                                                     |                                                                                  CACGATCTCAACCTATTATTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGTTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATCTGGGTGGATATGATTTTTAC  >  NZ_CP009273/385961‑386126

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑