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%	218.0 / NA	60	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 (34/26);  total (34/26)

GCACGATCTCAACCTATTATTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGTTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATCTGGGTGGATATGATTTTTACACT  >  NZ_CP009273/385960‑386129                                                                                      |                                                                                     gCACGATCTCAACCTATTATTTGAACCATGATTATGCGGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGa                                                                                  >  2:268204/1‑90 (MQ=255) gCACGATCTCAACCTATTATTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGa                                                                                  >  2:93995/1‑90 (MQ=255) gCACGATCTCAACCTATTATTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGa                                                                                  >  1:172480/1‑90 (MQ=255) gCACGATCTCAACCTATTATTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGa                                                                                  >  1:287191/1‑90 (MQ=255) gCACGATCTCAACCTATTATTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATCCAGTGATTCACGGCTCGa                                                                                  >  2:377733/1‑90 (MQ=255)   aCGATCTCAACCTATTATTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGAtt                                                                                <  1:252359/90‑1 (MQ=255)   aCGATCTCAACCTATTATTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGAtt                                                                                >  2:282112/1‑90 (MQ=255)   aCGATCTCAACCTATTATTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGAtt                                                                                <  1:520091/90‑1 (MQ=255)               tattatTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTAtgctg                                                                    >  2:106302/1‑90 (MQ=255)               tattatTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTAtgctg                                                                    <  2:112512/90‑1 (MQ=255)                attattTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTc                                                                           <  1:404396/82‑1 (MQ=255)                attattTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTAtgctgc                                                                   >  1:910646/1‑90 (MQ=255)                attattTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTAtgctgc                                                                   >  2:334739/1‑90 (MQ=255)                attattTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTAtgctgc                                                                   >  2:435675/1‑90 (MQ=255)                attattTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTAtgctgc                                                                   >  2:4500/1‑90 (MQ=255)                attattTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTAtgctgc                                                                   >  1:274025/1‑90 (MQ=255)                attattTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGAATATTTc                                                                           >  2:404396/1‑82 (MQ=255)                     ttGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGc                                                              <  1:457158/90‑1 (MQ=255)                     ttGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGc                                                              <  1:618066/90‑1 (MQ=255)                     ttGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGc                                                              <  1:141923/90‑1 (MQ=255)                      tGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCg                                                             >  1:714933/1‑90 (MQ=255)                      tGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCg                                                             >  1:785614/1‑90 (MQ=255)                       gAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGGTTACTTCTATGCTTCCTGGCgg                                                            >  2:510775/1‑90 (MQ=255)                       gAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCgg                                                            <  1:772697/90‑1 (MQ=255)                        aaCCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGt                                                           >  1:341364/1‑90 (MQ=255)                         aCCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGtt                                                          <  1:642527/90‑1 (MQ=255)                             tGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTAATTTTATGCTGCCTGGCGGttatta                                                      >  2:112115/1‑90 (MQ=255)                                 tATGCGGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGAt                                                  <  1:268204/90‑1 (MQ=255)                                  aTGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATc                                                 <  2:20189/90‑1 (MQ=255)                                       gACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTTTTTTTATCGtttt                                            >  2:25278/1‑90 (MQ=255)                                       gACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGtttt                                            >  1:617496/1‑90 (MQ=255)                                       gACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGtttt                                            >  2:87893/1‑90 (MQ=255)                                         cAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGa                                          >  1:356820/1‑90 (MQ=255)                                           gTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATg                                        >  2:841912/1‑90 (MQ=255)                                             aCTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCa                                      <  1:106302/90‑1 (MQ=255)                                                gCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATTCTCCCTGGAGGTTATTTAGATCGTTTTTATGCaatt                                   >  2:854417/1‑87 (MQ=255)                                                gCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGAt                                   <  2:910646/90‑1 (MQ=255)                                                gCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGAt                                   <  1:745766/90‑1 (MQ=255)                                                gCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGAt                                   <  1:518807/90‑1 (MQ=255)                                                gCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGAt                                   <  2:785614/90‑1 (MQ=255)                                                gCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGGTATTATGATCGTTTTGATGCAGAt                                   >  2:7111/1‑90 (MQ=255)                                                   aaTCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTTTTTTGATCGTTTTGATGCAGATTGt                                >  2:595584/1‑90 (MQ=255)                                                     tCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTTTGATCGTTTTGATGCAGATGGtaa                              >  2:560891/1‑90 (MQ=255)                                                     tCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGAt                                   <  1:804619/85‑1 (MQ=255)                                                     tCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGAt                                   >  2:804619/1‑85 (MQ=255)                                                     tCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGtaa                              <  1:556822/90‑1 (MQ=255)                                                       aGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGGTATTATGATCGTTTTGATGGAGATGGgaata                            >  1:818984/1‑90 (MQ=255)                                                                  aGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGGAATAATCTggggggg                 >  2:875178/1‑89 (MQ=255)                                                                    tAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATCTGGGTGGata               <  1:103585/90‑1 (MQ=255)                                                                      aTTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATCTGGGTGGATATg             <  1:32543/90‑1 (MQ=255)                                                                      aTTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATCTGGGTGGATATg             <  2:743978/90‑1 (MQ=255)                                                                      aTTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATCTGGGTGGATATg             <  2:223654/90‑1 (MQ=255)                                                                      aTTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATCTGGGTGGATATg             <  2:215874/90‑1 (MQ=255)                                                                      aTTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATCTGGGTGGATATg             <  1:875178/90‑1 (MQ=255)                                                                           gTGATTCACGGCTCGATTACTTCTTTGCTGCCTGGGGGTTATTTTGATCGGTTTGATGCAGATGGTAATAATCTGGGTGGATATGAtttt        >  2:40812/1‑90 (MQ=255)                                                                           gTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTTATGCAGATGGTAATAATCTGGGGGGATATGAtttt        >  2:911517/1‑90 (MQ=255)                                                                             gATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATCTGGGGGGATATGATTTTTa      >  1:77139/1‑90 (MQ=255)                                                                              aTTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATCTGGGTGGATATGATTTTTac     <  2:39567/90‑1 (MQ=255)                                                                               ttCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATCTGGGTGGATATGATTTTTaca    <  2:483579/90‑1 (MQ=255)                                                                                 cACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATCTGGGTGGATATGATTTTTACACt  >  1:308407/1‑90 (MQ=255)                                                                                      |                                                                                     GCACGATCTCAACCTATTATTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGTTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATCTGGGTGGATATGATTTTTACACT  >  NZ_CP009273/385960‑386129

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑