Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	340,444	(A)5→4	coding (558/816 nt)	BW25113_RS01680 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	340,440	0	A	.	98.0%	200.2 / ‑2.7	50	coding (554/816 nt)	BW25113_RS01680	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (0/1);  new base . (27/21);  total (28/22)
Fisher's exact test for biased strand distribution p-value = 4.49e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GTGCGAACAGATTGCAAATGTATTCTTCTTGAATACCATATGCCTTTGCTGAGAATTTTCCCTAAAGGGAAAGAGTGTATGCATGTGGAAAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGACGCGCCCATTAAGCAGGCGCTTGCGCATGGATTATTATTACACTT  >  NZ_CP009273/340352‑340524                                                                                         |                                                                                     gTGCGAACAGATTGCAAATGTATTCTTCTTGAATACCATATGCCTTTGCTGAGAATTTTCCCTAAAGGGAAAGAGTGTATGCATGTGGaa                                                                                     >  2:413584/1‑90 (MQ=255)   gCGAACAGATTGCAAATGTATTCTTCTTGAATACCATATGCCTTTGCTGAGAATTTTCCCTAAAGGGAAAGAGTGTATGCATGTGGaaaa                                                                                   <  1:1066194/90‑1 (MQ=255)   gCGAACAGATTGCAAATGTATTCTTCTTGAATACCATATGCCTTTGCTGAGAATTTTCCCTAAAGGGAAAGAGTGTATGCATGTGGaaaa                                                                                   <  1:1051596/90‑1 (MQ=255)           aTTGCAAATGTATTCTTCTTGAATACCATATGCCTTTGCTGAGAATTTTCCCTAAAGGGAAAGAGTGTATGCATGTGG‑AAAATGGCTTcg                                                                          >  1:356740/1‑90 (MQ=255)              gCAAATGTATTCTTCTTGAATACCATATGCCTTTGCTGAGAATTTTCCCTAAAGGGAAAGAGTGTATGCATGTGG‑AAAATGGCTTCGCGa                                                                       <  2:446096/90‑1 (MQ=255)                    gTATTCTTCTTGAATACCATATGCCTTTGCTGAGAATTTTCCCTAAAGGGAAAGAGTGTATGCATGTGG‑AAAATGGCTTCGCGAAATgtc                                                                 >  1:11856/1‑90 (MQ=255)                      aTTCTTCTTGAATACCATATGCCTTTGCTGAGAATTTTCCCTAAAGGGAAAGAGTGTATGCATGTGG‑AAAATGGCTTCGCGAAATgtcgt                                                               >  2:235646/1‑90 (MQ=255)                      aTTCTTCTTGAATACCATATGCCTTTGCTGAGAATTTTCCCTAAAGGGAAAGAGTGTATGCATGTGG‑AAAATGGCTTCGCGAAATgtcgt                                                               >  1:292441/1‑90 (MQ=255)                          ttcttGAATACCATATGCCTTTGCTGAGAATTTTCCCTAAAGGGAAAGAGTGTATGCATGTGG‑AAAATGGCTTCGCGAAATGTCGTCTAt                                                           <  1:424396/90‑1 (MQ=255)                              tGAATACCATATGCCTTTGCTGAGAATTTTCCCTAGAGGGAAAGAGTGTATGCATGTGG‑AAAATGGCTTCGCGAGATGTGGTCTATTCCg                                                       >  2:961838/1‑90 (MQ=255)                                  tACCATATGCCTTTGCTGAGAATTTTCCCTAAAGGGAAAGAGTGTATGCATGTGG‑AAAATGGCTTCGCGAAATg                                                                   >  2:828114/1‑74 (MQ=255)                                  tACCATATGCCTTTGCTGAGAATTTTCCCTAAAGGGAAAGAGTGTATGCATGTGG‑AAAATGGCTTCGCGAAATg                                                                   <  1:828114/74‑1 (MQ=255)                                    cgatatGCCTTTGCTGAGAATTTTCTCTAACGGAAAAGAGGGTATGCATGTAG‑AAAATGGTTTAGCGAAATGTCGTCTCTTCCGGagaca                                                 >  1:580228/3‑90 (MQ=255)                                    ccATATGCCTTTGCTGAGAATTTTCCCTAAAGGGAAAGAGTGTATGCATGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGagaca                                                 >  2:860115/1‑90 (MQ=255)                                      atatGCCTTTGCTGAGAATTTTCCCTAAAGGGAAAGAGTGTATGCATG‑GGGAAAATGGCTTCGCGAAAGGTCGGCTATTCCGGagacaga                                               >  2:611381/1‑90 (MQ=255)                                         tGCCTTTGCTGAGAATTTTCCCTAAAGGGAAAGAGTGTATGCATGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGAcgc                                            <  1:434906/90‑1 (MQ=255)                                           ccTTTGCTGAGAATTTTCCCTAAAGGGAAAGAGTGTATGCATGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGACgcgc                                          <  1:1076433/90‑1 (MQ=255)                                           ccTTTGCTGAGAATTTTCCCTAAAGGGAAAGAGTGTATGCATGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGACgcgc                                          <  1:990546/90‑1 (MQ=255)                                             tttGCTGAGAATTTTCCCTAAAGGGAAAGAGTGTATGCATGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGACGCGccc                                        >  1:914160/1‑90 (MQ=255)                                              ttGCTGAGAATTTTCCCTAAAGGGAAAGAGTGTATGCATGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGACGCGCCCa                                       >  2:326939/1‑90 (MQ=255)                                              ttGCTGAGAATTTTCCCTAAAGGGAAAGAGTGTATGCATGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGACGCGCCCa                                       >  1:405935/1‑90 (MQ=255)                                              ttGCTGAGAATTTTCCCTAAAGGGAAAGAGTGTATGCATGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGACGCGCCCa                                       >  2:61555/1‑90 (MQ=255)                                              ttGCTGAGAATTTTCCCTAAAGGGAAAGAGTGTATGCATGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGACGCGCCCa                                       >  2:1016211/1‑90 (MQ=255)                                                     gaATTTTCCCTAAAGGGAAAGAGTGTATGCATGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGACGCGCCCATTAAGCa                                >  2:1114662/1‑90 (MQ=255)                                                      aaTTTTCCCTAAAGGGAAAGAGTGTATGCATGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGACGCGCCCATTAAGCAg                               <  2:42799/90‑1 (MQ=255)                                                      aaTTTTCCCTAAAGGGAAAGAGTGTATGCATGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGACGCGCCCATTAAGCAg                               <  1:749804/90‑1 (MQ=255)                                                          ttCCCTAAAGGGAAAGAGTGTATGCATGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGACGCGCCCATTAAGCAGgcgc                           >  1:420091/1‑90 (MQ=255)                                                           tCCCTAAAGGGAAAGAGTGTATGCATGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGACGCGCCCATTAAGCAGGCGCt                          <  1:359140/90‑1 (MQ=255)                                                             ccTAAAGGGAAAGAGTGTATGCATGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGACGCGCCCATTAAGCAGGCGCTTg                        >  2:1137936/1‑90 (MQ=255)                                                               tAAAGGGAAAGAGTGTATGCATGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGACGCGCCCATTAAGCAGGCGCTTgcg                      >  2:864401/1‑90 (MQ=255)                                                                 aaGGGAAAGAGTGTATGCAGGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGACGCGCCCATTAAGCAGGCGCTTGCGCa                    <  1:971009/90‑1 (MQ=255)                                                                  aGGGAAAGAGTGTATGCATGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGACGCGCCCATTAAGCAGGCGCTTGCGCAt                   <  1:61555/90‑1 (MQ=255)                                                                  aGGGAAAGAGTGTATGCATGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGACGCGCCCATTAAGCAGGCGCTTGCGCAt                   <  1:1108061/90‑1 (MQ=255)                                                                  aGGGAAAGAGTGTATGCATGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGACGCGCCCATTAAGCAGGCGCTTGCGCAt                   <  2:133961/90‑1 (MQ=255)                                                                   gggAAAGAGTGTATGCATGTCGAAAAATTGGTTCGCGAGAGGTCGTCTATTGCGGAGACAGACGCGCCCATTAAGCAGGCGCTCGCGCAt                   <  1:1110837/90‑1 (MQ=255)                                                                       aaGAGTGTATGCATGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGACGCGCCCATTAAGCAGGCGCTTGCGCATGGatt              <  2:580228/90‑1 (MQ=255)                                                                       aaGAGTGTATGCATGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGACGCGCCCATTAAGCAGGCGCTTGCGCATGGatt              <  2:1206543/90‑1 (MQ=255)                                                                       aaGAGTGTATGCATGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGACGCGCCCATTAAGCAGGCGCTTGCGCATGGatt              <  1:806784/90‑1 (MQ=255)                                                                       aaGAGTGTATGCATGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGACGCGCCCATTAAGCAGGCGCTTGCGCATGGatt              <  1:472585/90‑1 (MQ=255)                                                                       aaGAGTGTATGCATGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGACGCGCCCATTAAGCAGGCGCTTGCGCATGGatt              <  2:405935/90‑1 (MQ=255)                                                                       aaGAGTGTATGCATGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGACGCGCCCATTAAGCAGGCGCTTGCGCATGGatt              <  1:1104036/90‑1 (MQ=255)                                                                            tgtATGCATGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGACGCGCCCAt                                      <  1:330401/61‑1 (MQ=255)                                                                            tgtATGCATGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGACGCGCCCAt                                      >  2:330401/1‑61 (MQ=255)                                                                            tgtATGCATGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGACGCGCCCATTAAGCAGGCGCTTGCGCATGGattattat         >  2:850117/1‑90 (MQ=255)                                                                            tgtATGCATGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGACGCGCCCATTAAGCAGGCGCTTGCGCATGGattattat         >  1:242766/1‑90 (MQ=255)                                                                             gtATGCATGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGACGCGCCCATTAAGCAGGCGCTTGCGCATGGattattatt        >  2:1147566/1‑90 (MQ=255)                                                                             gtATGCATGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGACGCGCCCATTAAGCAGGCGCTTGCGCATGGattattatt        >  1:960083/1‑90 (MQ=255)                                                                             gtATGCATGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGACGCGCCCATTAAGCAGGCGCTTGCGCATGGattattatt        >  1:634017/1‑90 (MQ=255)                                                                               aTGCATGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCTGAGACAGACGCGCCCATTAAGCAGGCGCTTGCGCATGGATTATTATTac      >  1:173217/1‑90 (MQ=255)                                                                                  cATGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGACGCGCCCATTAAGCAGGCGCTTGCGCATGGATTATTATTACACt   >  1:1083997/1‑90 (MQ=255)                                                                                   aTGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGACGCGCCCATTAAGCAGGCGCTTGCGCAt                   <  1:838469/73‑1 (MQ=255)                                                                                   aTGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGACGCGCCCATTAAGCAGGCGCTTGCGCAt                   >  2:838469/1‑73 (MQ=255)                                                                                   aTGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGACGCGCCCATTAAGCAGGCGCTTGCGCATGGATTATTATTACACtt  >  2:1020211/1‑90 (MQ=255)                                                                                         |                                                                                     GTGCGAACAGATTGCAAATGTATTCTTCTTGAATACCATATGCCTTTGCTGAGAATTTTCCCTAAAGGGAAAGAGTGTATGCATGTGGAAAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGACGCGCCCATTAAGCAGGCGCTTGCGCATGGATTATTATTACACTT  >  NZ_CP009273/340352‑340524

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑