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%	210.5 / NA	58	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 (29/29);  total (29/29)

GCACGATCTCAACCTATTATTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGTTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATCTGGGTGGATATGATTTTTACAC  >  NZ_CP009273/385960‑386128                                                                                      |                                                                                    gCACGATCTCAACCTATTATTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGa                                                                                 >  1:223949/1‑90 (MQ=255)   aCGATCTCAACCTATTATTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGAtt                                                                               <  1:256681/90‑1 (MQ=255)   aCGATCTCAACCTATTATTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGAtt                                                                               <  2:181296/90‑1 (MQ=255)           aaCCTATTATTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTAt                                                                       >  1:296103/1‑90 (MQ=255)             ccTATTATTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTAtgc                                                                     <  1:184122/90‑1 (MQ=255)                attattTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTAtgctgc                                                                  >  1:192908/1‑90 (MQ=255)                attattTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTAtgctgc                                                                  >  1:724489/1‑90 (MQ=255)                attattTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTAtgctgc                                                                  >  1:248655/1‑90 (MQ=255)                attattTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTAtgctgc                                                                  >  1:152351/1‑90 (MQ=255)                attattTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTAtgctgc                                                                  >  2:199097/1‑90 (MQ=255)                attattTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTAtgctgc                                                                  >  1:487235/1‑90 (MQ=255)                  tattTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCt                                                                >  2:645315/1‑90 (MQ=255)                   attTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTg                                                               <  2:540556/90‑1 (MQ=255)                   attTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTg                                                               <  1:644339/90‑1 (MQ=255)                   attTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTg                                                               <  1:42883/90‑1 (MQ=255)                     ttGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGc                                                             <  1:439536/90‑1 (MQ=255)                     ttGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGc                                                             <  2:561904/90‑1 (MQ=255)                     ttGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGc                                                             <  1:199097/90‑1 (MQ=255)                        aaCCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGt                                                          >  2:408948/1‑90 (MQ=255)                             tGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGttatta                                                     >  1:599217/1‑90 (MQ=255)                             tGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGttatta                                                     >  1:314329/1‑90 (MQ=255)                                 tATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGAt                                                 <  2:487235/90‑1 (MQ=255)                                 tATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGAt                                                 <  2:612773/90‑1 (MQ=255)                                  aTGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTTCCTGGCGGGTATTATGATc                                                >  2:507459/1‑90 (MQ=255)                                         cAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGa                                         >  2:697052/1‑90 (MQ=255)                                         cAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGa                                         >  1:671733/1‑90 (MQ=255)                                              cTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAg                                    <  2:67499/90‑1 (MQ=255)                                              cTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAg                                    <  1:651139/90‑1 (MQ=255)                                              cTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAg                                    <  1:341006/90‑1 (MQ=255)                                              cTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAg                                    <  1:366921/90‑1 (MQ=255)                                              cTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAg                                    <  2:509026/90‑1 (MQ=255)                                                gCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGGTCGTTTTGATGCAGAt                                  >  2:311300/1‑90 (MQ=255)                                                gCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGAt                                  <  2:429307/90‑1 (MQ=255)                                                gCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGAt                                  <  1:697052/90‑1 (MQ=255)                                                gCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGAt                                  <  2:671733/90‑1 (MQ=255)                                                gCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGAt                                  >  1:398641/1‑90 (MQ=255)                                                gCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGAt                                  <  1:627269/90‑1 (MQ=255)                                                     tCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGcc                                                                 >  1:66130/1‑54 (MQ=255)                                                     tCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGcc                                                                 <  2:346088/54‑1 (MQ=255)                                                     tCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGcc                                                                 >  1:346088/1‑54 (MQ=255)                                                     tCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGcc                                                                 <  2:66130/54‑1 (MQ=255)                                                     tCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGGTATTTTGATCGTTTTGATGCAGATGGgaa                             >  1:49910/1‑90 (MQ=255)                                                      cAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGtaat                            <  1:254943/90‑1 (MQ=255)                                                        gCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGGTATTATGATCGTTTTGATGCAGATGGtaataa                          >  1:635010/1‑90 (MQ=255)                                                          ttGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGc                                      <  2:639030/76‑1 (MQ=255)                                                          ttGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGc                                      <  2:658956/76‑1 (MQ=255)                                                          ttGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGc                                      >  1:639030/1‑76 (MQ=255)                                                          ttGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGc                                      >  1:658956/1‑76 (MQ=255)                                                               atCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATCTGGGt                   <  2:391345/90‑1 (MQ=255)                                                                  aGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCCGATGGGAATAATCTGGGGGGa                >  2:552699/1‑90 (MQ=255)                                                                  aGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATCTGGGTGGa                >  2:409645/1‑90 (MQ=255)                                                                  aGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATCTGGGTGGa                >  2:663516/1‑90 (MQ=255)                                                                    tAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATCTGGGTGGata              <  2:314329/90‑1 (MQ=255)                                                                     aaTTCAGTGATTCACGGCTCGGTTACTTCTATGCTGCCCGGGGGGTATTATGATCGTTTTGATGGAGATGGTAATAATCTGGGGGGatat             >  1:389242/1‑90 (MQ=255)                                                                      aTTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATCTGGGTGGATATg            <  2:497702/90‑1 (MQ=255)                                                                      aTTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATCTGGGTGGATATg            >  2:305089/1‑90 (MQ=255)                                                                           gTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATCTGGGTGGATATGAtttt       >  2:296709/1‑90 (MQ=255)                                                                                tCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATCTGGGTGGATATGATTTTTacac  <  1:663516/90‑1 (MQ=255)                                                                                      |                                                                                    GCACGATCTCAACCTATTATTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGTTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATCTGGGTGGATATGATTTTTACAC  >  NZ_CP009273/385960‑386128

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑