Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	386,451	T→C	pseudogene (745/1527 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	386,451	0	T	C	100.0%	188.4 / NA	52	pseudogene (745/1527 nt)	BW25113_RS01915	outer membrane autotransporter barrel domain‑containing protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (24/28);  total (24/28)

ACATCAATATTTCCAATAACTCCCGCGTTGCAGGTATTGCATTATCTCAAGGTAATACTTACAACGAAACCTACACTACCGAATCTCATACTTGGGATAACAATATCTCTGTAAAAGATTCCACAGTGACTTCGGGTTCAAATTATATCCTGGATAGCAATACTTATGGCAAAACTGGTCACTTTGGCAATTCTGATGAACCGAGTGATTATGCTGGCCCGGGTGATGTTGCAATGTCCTTTACTGCTTCAGGTTCCGACTATGC  >  NZ_CP009273/386320‑386584                                                                                                                                    |                                                                                                                                      aCATCAATATTTCCAATAACTCCCGCGTTGCAGGTATTGCATTATCTCAAGGTAATACTTACAACGAAACCTACACTACCGAATCTCATACTTGTGATAACAATATCTCTGTAAAAGATTCCACAGTGACTCCGGGTTc                                                                                                                                <  2:173036/139‑1 (MQ=255)  cATCAATATTTCCAATAACTCCCGCGTTGCAGGTATTGCATTATCTCAAGGTAATACTTACAACGAAACCTACACTACCGAATCTCATACTTGGGATAACAATATCTCTGTAAAAGATTCCACAGTGACTCCGGGTTc                                                                                                                                >  2:777785/1‑138 (MQ=255)          tttCCAATAACTCCCGCGTTGCAGGTATTGCATTATCTCAAGGTAATACTTACAACGAAACCTACACTACCGAATCTCATACTTGGGATAACAATATCTCTGTAAAAGATTCCACAGTGACTCCGGGTTCAAATtata                                                                                                                        <  1:657595/138‑1 (MQ=255)            tCCAATAACACCCGCGTTGCAGGTATTGCATTATCTCAAGGTAATACTTACAACGAAACCTACACTACCGAATCTCATACTTGGGATAACAATATCTCTGTAAAAGATTCCACAGTGACTCCGGGTTCAAATTATATc                                                                                                                      <  1:139571/138‑1 (MQ=255)             ccAATAACTCCCGCGTTGCAGGTATTGCATTATCTCAAGGTAATACTTACAACGAAACCTACACTACCGAATCTCATACTTGGGATAACAATATCTCTGTAAAAGATTCCACAGTGACTCCGGGTTCAAATTATATCCt                                                                                                                    >  2:496036/1‑139 (MQ=255)              cAATAACTCCCGCGTTGCAGGTATTGCATTATCTCAAGGTAATACTTACAACGAAACCTACACTACCGAATCTCATACTTGGGATAACAATATCTCTGTAAAAGATTCCACAGTGACTCCGGGTTCAAATTATATCCTg                                                                                                                   <  1:463141/139‑1 (MQ=255)               aaTAACTCCCGCGTTGCAGGTATTGCATTATCTCAAGGTAATACTTACAACGAAACCTACACTACCGAATCTCATACTTGGGATAACAATATCTCTGTAAAAGATTCCACAGTGACTCCGGGTTCAAATTATATCCTgg                                                                                                                  <  2:692621/139‑1 (MQ=255)                aTAACTCCCGCGTTGCAGGTATTGCATTATCTCAAGGTAATACTTACAACGAAACCTACACTACCGAATCTCATACTTGGGATAACAATATCTCTGTAAAAGATTCCACAGTGACTCCGGGTTCAAATTATATCCTGGa                                                                                                                 <  2:87223/139‑1 (MQ=255)                          cgTTGCAGGTATTGCATTATCTCAAGGTAATACTTACAACGAAACCTACACTACCGAATCTCATACTTGGGATAACAATATCTCTGTAAAAGATTCCACAGTGACTCCGGGTTCAAATTATATCCTGGATAGCAATACt                                                                                                       <  1:168762/139‑1 (MQ=255)                          cgTTGCAGGTATTGCATTATCTCAAGGTAATACTTACAACGAAACCTACACTACCGAATCTCATACTTGGGATAACAATATCTCTGTAAAAGATTCCACAGTGACTCCGGGTTCAAATTATATCCTGGATAGCAATACt                                                                                                       <  1:290556/139‑1 (MQ=255)                                                 aaGGTAATACTTACAACGAAACCTACACTACCGAATCTCATACTTGGGATAACAATATCTCTGTAAAAGATTCCACAGTGACTCCGGGTTCAAATTATATCCTGGATAGCAATACTTATGGCAAAACTGGTCACttt                                                                                  <  1:741855/137‑1 (MQ=255)                                                  aGGTAATACTTACAACGAAACCTACACTACCGAATCTCATACTTGGGATAACAATATCTCTGTAAAAGATTCCACAGTGACTCCGGGTTCAAATTATATCCTGGATAGCAATACTTATGGCAAAACTGGTCACTTTgg                                                                                >  1:46130/1‑138 (MQ=255)                                                   ggTAATACTTACAACGAAACCTACACTACCGAATCTCATACTTGGGATAACAATATCTCTGTAAAAGATTCCACAGTGACTCCGGGTTCAAATTATATCCTGGATAGCAATACTTATGGCAAAACTGGTCACTTTGGc                                                                               >  2:105617/1‑138 (MQ=255)                                                    gTAATACTTACAACGAAACCTACACTACCGAATCTCATACTTGGGATAACAATATCTCTGTAAAAGATTCCACAGTGACTCCGGGTTCAAATTATATCCTGGATAGCAATACTTATGGCAAAACTGGTCACTTTGGCaa                                                                             <  2:90258/139‑1 (MQ=255)                                                        tACTTACAACGAAACCTACACTACCGAATCTCATACTTGGGATAACAATATCTCTGTAAAAGATTCCACAGTGACTCCGGGTTCAAATTATATCCTGGATAGCa                                                                                                            >  2:332023/1‑104 (MQ=255)                                                        tACTTACAACGAAACCTACACTACCGAATCTCATACTTGGGATAACAATATCTCTGTAAAAGATTCCACAGTGACTCCGGGTTCAAATTATATCCTGGATAGCa                                                                                                            <  1:332023/104‑1 (MQ=255)                                                        tACTTACAACGAAACCTACACTACCGAATCTCATACTTGGGATAACAATATCTCTGTAAAAGATTCCACAGTGACTCCGGGTTCAAATTATATCCTGGATAGCAATACTTATGGCAAAACTGGTCACTTTGGCAATTCt                                                                         >  2:515241/1‑139 (MQ=255)                                                                 cGAAACCTACACTACCGAATCTCATACTTGGGATAACAATATCTCTGTAAAAGATTCCACAGTGACTCCGGGTTCAAATTATATCCTGGATAGCAATACTTATGGCAAAACTGGTCACTTTGGCAATTCTGATGAACCg                                                                <  2:836191/139‑1 (MQ=255)                                                                                cGAATCTCATACTTGGGATAACAATATCTCTGTAAAAGATTCCACAGTGACTCCGGGTTCAAATTATATCCTGGATAGCAATACTTATGGCAAAACTGGTCACTTTGGCAATTCTGATGAACCGAGTGATTATGCTGGc                                                 <  1:841403/139‑1 (MQ=255)                                                                                       cATACTTGGGATAACAATATCTCTGTAAAAGATTCCACAGTGACTCCGGGTTCAAATTATATCCTGGATAGCAATACTTATGGCAAAACTGGTCACTTTGGCAATTCTGATGAACCGAGTGATTATGCTGGCCCGGGt                                           >  2:661624/1‑138 (MQ=255)                                                                                        aTACTTGGGATAACAATATCTCTGTAAAAGATTCCACAGTGACTCCGGGTTCAAATTATATCCTGGATAGCAATACTTATGGCAAAACTGGTCACTTTGGCAATTCTGATGAACCGAGTGATTATGCTGGCCCggg                                            <  1:543700/136‑1 (MQ=255)                                                                                         tACTTGGGATAACAATATCTCTGTAAAAGATTCCACAGTGACTCCGGGTTCAAATTATATCCTGGATAGCAATACTTATGGCAAAACTGGTCACTTTGGCAATTCTGATGAACCGAGTGATTATGCTGGCCCGGGTGAt                                        <  1:496036/139‑1 (MQ=255)                                                                                         tACTTGGGATAACAATATCTCTGTAAAAGATTCCACAGTGACTCCGGGTTCAAATTATATCCTGGATAGCAATACTTATGGCAAAACTGGTCACTTTGGCAATTCTGATGAACCGAGTGATTATGCTGGCCCGGGTGAt                                        >  2:75079/1‑139 (MQ=255)                                                                                              gggATAACAATATCTCTGTAAAAGATTCCACAGTGACTCCGGGTTCAAATTATATCCTGGATAGCAATACTTATGGCAAAACTGGTCAc                                                                                     <  1:54352/89‑1 (MQ=255)                                                                                              gggATAACAATATCTCTGTAAAAGATTCCACAGTGACTCCGGGTTCAAATTATATCCTGGATAGCAATACTTATGGCAAAACTGGTCAc                                                                                     >  2:54352/1‑89 (MQ=255)                                                                                              gggATAACAATATCTCTGTAAAAGATTCCACAGTGACTCCGGGTTCAAATTATATCCTGGATAGCAATACTTATGGCAAAACTGGTCACTTTGGCAATTCTGATGAACCGAGTGATTATGCTGGCCCGGGTGATGTTg                                    >  2:658735/1‑138 (MQ=255)                                                                                              gggATAACAATATCTCTGTAAAAGATTCCACAGTGACTCCGGGTTCAAATTATATCCTGGATAGCAATACTTATGGCAAAACTGGTCACTTTGGCAATTCTGATGAACCGAGTGATTATGCTGGCCCGGGTGATGTTg                                    >  2:554214/1‑138 (MQ=255)                                                                                               ggATAACAATATCTCTGTAAAAGATTCCACAGTGACTCCGGGTTCAAATTATATCCTGGATAGCAATACTTATGGCAAAACTGGTCACTTTGGCAATTCTGATGAACCGAGTGATTATGCTGGCCCGGGTGATGTTGCa                                  <  1:266821/139‑1 (MQ=255)                                                                                               ggATAACAATATCTCTGTAAAAGATTCCACAGTGACTCCGGGTTCAAATTATATCCTGGATAGCAATACTTATGGCAAAACTGGTCACTTTGGCAATTCTGATGAACCGAGTGATTATGCTGGCCCGGGTGATGTTGCa                                  <  1:661624/139‑1 (MQ=255)                                                                                                 aTAACAATATCTCTGTAAAAGATTCCACAGTGACTCCGGGTTCAAATTATATCCTGGATAGCAATACTTATGGCAAAACTGGTCACTTTGGCAATTCTGATGAACCGAGTGATTATGCTGGCCCGGGTGATGTTGCAAt                                >  1:187000/1‑139 (MQ=255)                                                                                                 aTAACAATATCTCTGTAAAAGATTCCACAGTGACTCCGGGTTCAAATTATATCCTGGATAGCAATACTTATGGCAAAACTGGTCACTTTGGCAATTCTGATGAACCGAGTGATTATGCTGGCCCGGGTGATGTTGCAAt                                <  2:661667/139‑1 (MQ=255)                                                                                                    aCAATATCTCTGTAAAAGATTCCACAGTGACTCCGGGTTCAAATTATATCCTGGATAGCAATACTTATGGCAAAACTGGTCACTTTGGCAATTCTGATGAACCGAGTGATTATGCTGGCCCGGGTGATGTTGCAATGTc                             >  1:44579/1‑139 (MQ=255)                                                                                                        tatCTCTGTAAAAGATTCCACAGTGACTCCGGGTTCAAATTATATCCTGGATAGCAATACTTATGGCAAAACTGGTCACTTTGGCAATTCTGATGAACCGAGTGATTATGCTGGCCCGGGTGATGTTGCAATGTCCttt                         <  2:789560/139‑1 (MQ=255)                                                                                                          tctcTGTAAAAGATTCCACAGTGACTCCGGGTTCAAATTATATCCTGGATAGCAATACTTATGGCAAAACTGGTCACTTTGGCAATTCTGATGAACCGAGTGATTATGCTGGCCCGGGTGATGTTGCAATGTCCTTTAc                       >  2:474835/1‑139 (MQ=255)                                                                                                          tctcTGTAAAAGATTCCACAGTGACTCCGGGTTCAAATTATATCCTGGATAGCAATACTTATGGCAAAACTGGTCACTTTGGCAATTCTGATGAACCGAGTGATTATGCTGGCCCGGGTGATGTTGCAATGTCCTTTAc                       >  2:644911/1‑139 (MQ=255)                                                                                                          tctcTGTAAAAGATTCCACAGTGACTCCGGGTTCAAATTATATCCTGGATAGCAATACTTATGGCAAAACTGGTCACTTTGGCAATTCTGATGAACCGAGTGATTATGCTGGCCCGGGTGATGTTGCAATGTCCTTTAc                       >  1:708287/1‑139 (MQ=255)                                                                                                              tGTAAAAGATTCCACAGTGACTCCGGGTTCAAATTATATCCTGGATAGCAATACTTATGGCAAAACTGGTCACTTTGGCAATTCTGATGAACCg                                                                >  1:543688/1‑94 (MQ=255)                                                                                                              tGTAAAAGATTCCACAGTGACTCCGGGTTCAAATTATATCCTGGATAGCAATACTTATGGCAAAACTGGTCACTTTGGCAATTCTGATGAACCg                                                                <  2:543688/94‑1 (MQ=255)                                                                                                              tGTAAAAGATTCCACAGTGACTCCGGGTTCAAATTATATCCTGGATAGCAATACTTATGGCAAAACTGGTCACTTTGGCAATTCTGATGAACCGAGTGATTATGCTGGCCCGGGTGATGTTGCa                                  <  2:718845/124‑1 (MQ=255)                                                                                                              tGTAAAAGATTCCACAGTGACTCCGGGTTCAAATTATATCCTGGATAGCAATACTTATGGCAAAACTGGTCACTTTGGCAATTCTGATGAACCGAGTGATTATGCTGGCCCGGGTGATGTTGCa                                  >  1:718845/1‑124 (MQ=255)                                                                                                              tGTAAAAGATTCCACAGTGACTCCGGGTTCAAATTATATCCTGGATAGCAATACTTATGGCAAAACTGGTCACTTTGGCAATTCTGATGAACCGAGTGATTATGCTGGCCCGGGTGATGTTGCAATGTCCTTTACTGCt                   >  2:621725/1‑139 (MQ=255)                                                                                                                tAAAAGATTCCACAGTGACTCCGGGTTCAAATTATATCCTGGATAGCAATACTTATGGCAAAACTGGTCACTTTGGCAATTCTGATGAACCGAGTGATTATGCTGGCCCGGGTGATGTTGCAATGTCCTTTACTGCtt                  <  1:515241/138‑1 (MQ=255)                                                                                                                tAAAAGATTCCACAGTGACTCCGGGTTCAAATTATATCCTGGATAGCAATACTTATGGCAAAACTGGTCACTTTGGCAATTCTGATGAACCGAGTGATTATGCTGGCCCGGGTGATGTTGCAATGTCCTTTACTGCtt                  <  2:46130/138‑1 (MQ=255)                                                                                                                tAAAAGATTCCACAGTGACTCCGGGTTCAAATTATATCCTGGATAGCAATACTTATGGCAAAACTGGTCACTTTGGCAATTCTGATGAACCGAGTGATTATGCTGGCCCGGGTGATGTTGCAATGTCCTTTACTGCtt                  <  2:387597/138‑1 (MQ=255)                                                                                                                        tCCACAGTGACTCCGGGTTCAAATTATATCCTGGATAGCAATACTTATGGCAAAACTGGTCACTTTGGCAATTCTGATGAACCGAGTGATTATGCTGGCCCggg                                            >  1:554991/1‑104 (MQ=255)                                                                                                                        tCCACAGTGACTCCGGGTTCAAATTATATCCTGGATAGCAATACTTATGGCAAAACTGGTCACTTTGGCAATTCTGATGAACCGAGTGATTATGCTGGCCCggg                                            <  2:554991/104‑1 (MQ=255)                                                                                                                        tCCACAGTGACTCCGGGTTCAAATTATATCCTGGATAGCAATACTTATGGCAAAACTGGTCACTTTGGCAATTCTGATGAACCGAGTGATTATGCTGGCCCGGGTGATGTTGCAATGTCCTTTACTGCTTCAGGTTcc          >  2:69783/1‑138 (MQ=255)                                                                                                                          cacaGTGACTCCGGGTTCAAATTATATCCTGGATAGCAATACTTATGGCAAAACTGGTCACTTTGGCAATTCTGATGAACCGAGTGATTATGCTGGCCCGGGTGATGTTGCAATGTCCTTTACTGCTTCAGGTTCCGa        <  1:644911/138‑1 (MQ=255)                                                                                                                          cacaGTGACTCCGGGTTCAAATTATATCCTGGATAGCAATACTTATGGCAAAACTGGTCACTTTGGCAATTCTGATGAACCGAGTGATTATGCTGGCCCGGGTGATGTTGCAATGTCCTTTACTGCTTCAGGTTCCGAc       >  1:265529/1‑139 (MQ=255)                                                                                                                          cacaGTGACTCCGGGTTCAAATTATATCCTGGATAGCAATACTTATGGCAAAACTGGTCACTTTGGCAATTCTGATGAACCGAGTGATTATGCTGGCCCGGGTGATGTTGCAATGTCCTTTACTGCTTCAGGTTCCGAc       >  2:854042/1‑139 (MQ=255)                                                                                                                           acaGTGACTCCGGGTTCAAATTATATCCTGGATAGCAATACTTATGGCAAAACTGGTCACTTTGGCAATTCTGATGAACCGAGTGATTATGCTGGCCCGGGTGATGTTGCAATGTCCTTTACTGCTTCAGGTTCCGACt      <  1:777785/139‑1 (MQ=255)                                                                                                                               tGACTCCGGGTTCAAATTATATCCTGGATAGCAATACTTATGGCAAAACTGGTCACTTTGGCAATTCTGATGAACCGAGTGATTATGCTGGCCCGGGTGATGTTGCAATGTCCTTTACTGCTTCAGGTTCCGACTATGc  >  1:729111/1‑139 (MQ=255)                                                                                                                                    |                                                                                                                                      ACATCAATATTTCCAATAACTCCCGCGTTGCAGGTATTGCATTATCTCAAGGTAATACTTACAACGAAACCTACACTACCGAATCTCATACTTGGGATAACAATATCTCTGTAAAAGATTCCACAGTGACTTCGGGTTCAAATTATATCCTGGATAGCAATACTTATGGCAAAACTGGTCACTTTGGCAATTCTGATGAACCGAGTGATTATGCTGGCCCGGGTGATGTTGCAATGTCCTTTACTGCTTCAGGTTCCGACTATGC  >  NZ_CP009273/386320‑386584

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑