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	.	94.0%	184.2 / 8.0	50	coding (554/816 nt)	BW25113_RS01680	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (2/1);  new base . (24/23);  total (26/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.53e-01

CGAACAGATTGCAAATGTATTCTTCTTGAATACCATATGCCTTTGCTGAGAATTTTCCCTAAAGGGAAAGAGTGTATGCATGTGGAAAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGACGCGCCCATTAAGCAGGCGCTT‑‑GCGCATGGATTATTATTACACTTA  >  NZ_CP009273/340355‑340525                                                                                      |                                                                                        cGAACAGATTGCAAATGTATTCTTCTTGAATACCATATGCCTTTGCTGAGAATTTTCCCTAAAGGGAAAGAGTGTATGCATGTGGaaaat                                                                                     <  2:196386/90‑2 (MQ=255)        aTTGCAAATGTATTCTTCTTGAATACCATATGCCTTTGCTGAGAATTTTCCCTAAAGGGAAAGAGTGTATGCATGTGG‑AAAATGGCTTcg                                                                             >  1:967576/1‑90 (MQ=255)           gCAAATGTATTCTTCTTGAATACCATATGCCTTTGCTGAGAATTTTCCCTAAAGGGAAAGAGTGTATGCATGTGG‑AAAATGGCTTCGCGa                                                                          <  2:21085/90‑1 (MQ=255)             aaaTGTATTCTTCTTGAATACCATATGCCTTTGCTGAGAATTTTCCCTAAAGGGAAAGAGTGTATGCATGTGG‑AAAATGGCTTCGCGaaa                                                                        <  2:481542/90‑1 (MQ=255)                tGTATTCTTCTTGAATACCATATGCCTTTGCTGAGAATTTTCCCTAAAGGGAAAGAGTGTATGCATGTGG‑AAAATGGCTTCGCGAAATgt                                                                     <  1:812744/90‑1 (MQ=255)                 gtcttcttcCTGAATACCATATGCCGTTGCTGAGAATTTTCGCTAAAGGGAAAAAGCGTATCCATGAGG‑AACATGGCTTCGCGAAAGgtg                                                                    >  1:844126/4‑89 (MQ=255)                    ttcttcTTGAATACCATATGCCTTTGCTGAGAATTTTCCCTAAAGGGAAAGAGTGTATGCATGTGG‑AAAATGGCTTCGCGAAATgtcgtc                                                                 <  1:634149/90‑1 (MQ=255)                    ttcttcTTGAATACCATATGCCTTTGCTGAGAATTTTCCCTAAAGGGAAAGAGTGTATGCATGTGG‑AAAATGGCTTCGCGAAATgtcgtc                                                                 <  1:631263/90‑1 (MQ=255)                        tcttGAATACCATATGCCTTTGCTGAGAATTTTCCCTAAAGGGAAAGAGTGTATGCATGTGG‑AAAATGGCTTCGCGAAATGTCGTCTAtt                                                             >  1:471560/1‑90 (MQ=255)                           tGAATACCATATGCCTTTGCTGAGAATTTTCCCTAAAGGGAAAGAGTGTATGCATGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCg                                                          >  1:122985/1‑90 (MQ=255)                                   atatGCCTTTGCTGAGAATTTTCCCTAAAGGGAAAGAGTGTATGCATGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGagacaga                                                  >  2:384017/1‑90 (MQ=255)                                   atatGCCTTTGCTGAGAATTTTCCCTAAAGGGAAAGAGTGTATGCATGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGagacaga                                                  >  1:46900/1‑90 (MQ=255)                                       gCCTTTGCTGAGAATTTTCCCTAAAGGGAAAGAGTGTATGCATGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGAcgcg                                              <  1:632590/90‑1 (MQ=255)                                       gCCTTTGCTGAGAATTTTCCCTAAAGGGAAAGAGTGTATGCATGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGAcgcg                                              <  2:471560/90‑1 (MQ=255)                                       gCCTTTGCTGAGAATTTTCCCTAAAGGGAAAGAGTGTATGCATGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGAcgcg                                              <  1:930987/90‑1 (MQ=255)                                        ccTTTGCTGAGAATTTTCCCTAAAGGGAAAGAGTGTATGCATGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGACgcgc                                             <  2:839961/90‑1 (MQ=255)                                        ccTTTGCTGAGAATTTTCCCTAAAGGGAAAGAGTGTATGCATGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGACgcgc                                             <  2:316774/90‑1 (MQ=255)                                        ccTTTGCTGAGAATTTTCCCTAAAGGGAAAGAGTGTATGCATGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGACgcgc                                             >  1:316774/1‑90 (MQ=255)                                          tttGCTGAGAATTTTCCCTAAAGGGAAAGAGTGTATGCATGTGG‑AAAATGGCTTCGCGAAATgtcgtc                                                                 >  1:81174/1‑68 (MQ=255)                                          tttGCTGAGAATTTTCCCTAAAGGGAAAGAGTGTATGCATGTGG‑AAAATGGCTTCGCGAAATgtcgtc                                                                 <  2:81174/68‑1 (MQ=255)                                           ttGCTGAGAATTTTCCCTAAAGGGAAAGAGTGTATGCATGTGGAAAAATGGCTTCGCGAAATGTCGTCTATTCCGGagac                                                     >  1:550056/1‑80 (MQ=255)                                           ttGCTGAGAATTTTCCCTAAAGGGAAAGAGTGTATGCATGTGGAAAAATGGCTTCGCGAAATGTCGTCTATTCCGGagac                                                     <  2:550056/80‑1 (MQ=255)                                           ttGCTGAGAATTTTCCCTAAAGGGAAAGAGTGTATGCATGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGAcgcg                                              >  1:945680/1‑86 (MQ=255)                                           ttGCTGAGAATTTTCCCTAAAGGGAAAGAGTGTATGCATGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGAcgcg                                              <  2:945680/86‑1 (MQ=255)                                           ttGCTGAGAATTTTCCCTAAAGGGAAAGAGTGTATGCATGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGACGCGCCCa                                          >  2:32587/1‑90 (MQ=255)                                           ttGCTGAGAATTTTCCCTAAAGGGAAAGAGTGTATGCATGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGACGCGCCCa                                          >  2:375532/1‑90 (MQ=255)                                           ttGCTGAGAATTTTCCCTAAAGGGAAAGAGTGTATGCATGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGACGCGCCCa                                          >  1:212268/1‑90 (MQ=255)                                           ttGCTGAGAATTTTCCCTAAAGGGAAAGAGTGTATGCATGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGACGCGCCCa                                          >  2:248662/1‑90 (MQ=255)                                           ttGCTGAGAATTTTCCCTAAAGGGAAAGAGTGTATGCATGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGACGCGCCCa                                          >  2:214029/1‑90 (MQ=255)                                           ttGCTGAGAATTTTCCCTAAAGGGAAAGAGTGTATGCATGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGACGCGCCCa                                          >  2:19600/1‑90 (MQ=255)                                            tGCTGAGAATTTTCCCTAAAGGGAAAGAGTGTATGCATGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGACGCGCCCAt                                         <  1:248662/90‑1 (MQ=255)                                              cTGAGAATTTTCCCTAAAGGGAAAGAGTGTATGCATGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGACGCGCCCATTa                                       <  2:422846/90‑1 (MQ=255)                                                  gaATTTTCCCTAAAGGGAAAGAGTGTATGCATGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGACGCGCCCATTAAGCa                                   <  2:770369/90‑1 (MQ=255)                                                            tAAAGGGAAAGAGTGTATGCATGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGACGCGCCCATTAAGCAGGCGCTT‑‑gcg                       >  2:931876/1‑90 (MQ=255)                                                              aaGGGAAAGAGTGTATGCATGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGACGCGCCCATTAAGCAGGCGCTT‑‑gcgcg                     <  2:122985/90‑2 (MQ=255)                                                               aGGGAAAGAGTGTATGCATGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGACGCGCCCATTAAGCAGGCGCTT‑‑GCGCAt                    <  2:806506/90‑1 (MQ=255)                                                               aGGGAAAGAGTGTATGCATGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGACGCGCCCATTAAGCAGGCGCTT‑‑GCGCAt                    <  1:855689/90‑1 (MQ=255)                                                               aGGGAAAGAGTGTATGCATGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGACGCGCCCATTAAGCAGGCGCTT‑‑GCGCAt                    <  1:790265/90‑1 (MQ=255)                                                               aGGGAAAGAGTGTATGCATGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGACGCGCCCATTAAGCAGGCGCTT‑‑GCGCAt                    <  2:691059/90‑1 (MQ=255)                                                                       agTGTATGCATGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGACGCGCCCATTAAGCAGGCGCTT‑‑GCGCATGGattatt            >  2:544999/1‑90 (MQ=255)                                                                          gtATGCATGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGACGCGCCCATTAAGCAGGCGCTT‑‑GCGCATGGattattatt         >  1:907130/1‑90 (MQ=255)                                                                           tATGCATGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGACGCGCCCATTAAGCAGGCGCTT‑‑GCGCATGGAttattatta        >  2:706095/1‑90 (MQ=255)                                                                            aTGCATGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGACGCGCCCATTAAGCAGGCGCTTGCGCGCATGGattattatt         >  2:172222/1‑90 (MQ=255)                                                                            aTGCATGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGACGCGCCCATTAAGCAGGCGCTT‑‑gc                        <  2:524779/73‑1 (MQ=255)                                                                            aTGCATGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGACGCGCCCATTAAGCAGGCGCTT‑‑gc                        >  1:524779/1‑73 (MQ=255)                                                                            aTGCATGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGACGCGCCCATTAAGCAGGCGCTT‑‑GCGCATGGATTATTATTac       <  1:824193/90‑1 (MQ=255)                                                                               cATGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGACGCGCCCATTAAGCAGGCGCTT‑‑GCGCATGGATTATTATTACACt    <  2:967576/90‑1 (MQ=255)                                                                                aTGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGACGCGCCCATTAAGCAGGCGCTT‑‑GCGCATGGATTATTATTACACtt   >  2:237414/1‑90 (MQ=255)                                                                                aTGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGACGCGCCCATTAAGCAGGCGCTT‑‑GCGCATGGATTATTATTACACtt   >  2:149174/1‑90 (MQ=255)                                                                                aTGTGG‑AAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGACGCGCCCATTAAGCAGGCGCTT‑‑GCGCATGGATTATTATTACACtt   >  1:382737/1‑90 (MQ=255)                                                                                  gtgGAAAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGACGCGCCCATTAAGCAGGCGCTT‑‑GCGCATGGATTATTATTACACTTa  >  1:251811/1‑90 (MQ=255)                                                                                      |                                                                                        CGAACAGATTGCAAATGTATTCTTCTTGAATACCATATGCCTTTGCTGAGAATTTTCCCTAAAGGGAAAGAGTGTATGCATGTGGAAAAATGGCTTCGCGAAATGTCGTCTATTCCGGAGACAGACGCGCCCATTAAGCAGGCGCTT‑‑GCGCATGGATTATTATTACACTTA  >  NZ_CP009273/340355‑340525

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑