Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092734,612,0670AG52.4% 14.1 / 23.2 21E161G (GAG→GGG) yjjJtype II toxin‑antitoxin system HipA family toxin YjjJ
Reads supporting (aligned to +/- strand):  ref base A (3/7);  new base G (11/0);  total (14/7)
Fisher's exact test for biased strand distribution p-value = 1.03e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.23e-03
Rejected as consensus: Frequency below/above cutoff threshold.

TGATGATATACGTCTCTGGCAGGAAGAAGATGTGCTCTACGCCCTGACCGTATTTAACGGTGAATATACTGGCGGTTGGTTGGTCGGGGAGGGGAATTATCAGCGATGGATTACTGCACAACACCCTGCGGAAATTCCTCTGGATCAAAAACTCACCCATTACGAACAGCTGGCA  >  NZ_CP009273/4611978‑4612152
                                                                                         |                                                                                     
tgatgaTATACGTCTCTGGCAGGAAGAAGATGTGCTCTACGCCCTGACCGTATTTAACGGTGAATATACTGGCGGTTGGTTGGTCgggga                                                                                       <  2:209189/90‑1 (MQ=255)
   tgatATACGTCTCTGGCAGGAAGAAGATGTGCTCTACGCCCTGACCGTATTTAACGGTGAATATACTGGCGGTTGGTTGGTCggggaggg                                                                                    <  2:205512/90‑1 (MQ=255)
           gTCTCTGGCAGGAAGAAGATGTGCTCTACGCCCTGACCGTATTTAACGGTGAATATACTGGCGGTTTGTTTGGCGGGGGGGGGAATTATc                                                                            >  1:91880/1‑90 (MQ=255)
             ctctGGCAGGAAGAAGATGTGCTCTACGCCCTGACCGTATTTAACGGTGAATATACTGGCGGTTGGTTGGTCGGGGGGGGGGATTATCAg                                                                          >  1:392077/1‑90 (MQ=255)
             ctctGGCAGGAAGAAGATGTGCTCTACGCCCTGACCGTATTTAACGGTGAATATACTGGCGGTTGGGTGGTCGGGGGGGGGGATTATCAg                                                                          >  2:538972/1‑90 (MQ=255)
             ctctGGCAGGAAGAAGATGTGCTCTACGCCCTGACCGTATTTAACGGTGAATATACTGGCGGGTGGGTGGGCGGGGGGGGGGATTATCAg                                                                          >  1:314820/1‑90 (MQ=255)
               ctGGCAGGAAGAAGATGTGCTCTACGCCCTGACCGTATTTAACGGTGAATATACTGGCGGTTGGTTGGTCGGGGAGGGGAATTATc                                                                            <  1:255365/86‑1 (MQ=255)
               ctGGCAGGAAGAAGATGTGCTCTACGCCCTGACCGTATTTAACGGTGAATATACTGGCGGTTGGTTGGTCGGGGAGGGGAATTATc                                                                            >  2:255365/1‑86 (MQ=255)
               ctGGCAGGAAGAAGATGTGCTCTACGCCCTGACCGTATTTAACGGTGAATATACTGGCGGTTGGGTGGTCGGGGGGGGGGATTATCAGCg                                                                        >  2:468167/1‑90 (MQ=255)
                     ggAAGAAGATGTGCTCTACGCCCTGACCGTATTTAACGGTGAATATACTGGCGGTTGGGTGGGCGGGGGGGGGGATTATTAGCGATgggt                                                                  >  2:483162/1‑88 (MQ=255)
                          aagaTGTGCTCTACGCCCTGACCGTATTTAACGGTGAATATACTGGCGGTTGGTTGGTCGGGGAGGGGAATTATCAGCGATGGATTACTg                                                             <  2:519521/90‑1 (MQ=255)
                                    ctACGCCCTGACCGTATTTAACGGTGAATATACTGGCGGTTGGTTGGTCGGGGAGGGGAATTATCAGCGATGGATTACTGCACAACAccc                                                   <  2:91880/90‑1 (MQ=255)
                                    ctACGCCCTGACCGTATTTAACGGTGAATATACTGGCGGTTGGTTGGTCGGGGAGGGGAATTATCAGCGATGGATTACTGCACAACAccc                                                   <  2:392077/90‑1 (MQ=255)
                                      aCGCCCTGACCGTATTTAACGGTGAATATACTGGCGGTTGGTTGGTCGGGGGGGGGAATTATCAGCGATGGATTACTGCACAAAAccccg                                                 >  2:409005/1‑88 (MQ=255)
                                           cTGACCGTATTTAACGGTGAATATACTGGCGGGTGGTTGGTCGGGGGGGGGGATTATTAGCGAGGGATTTGTGGTCAACACCCTGCggga                                            >  1:456084/1‑88 (MQ=255)
                                                           gTGAATATACTGGCGGTTTGTTGGTCGGGGAGGGGGATTATTCCCGATGGGTTAATGACAAACACCCCTCGGAAATTTCTCTTGATCaaa                            >  2:450659/1‑90 (MQ=255)
                                                             gAATATACTGGCGGTTGGTTGGTCGGGGGGGGGAATTATCAGCGATGGATTACTGCACAACACCCTGCGGAAATTTCTCTGGATCaaaaa                          >  2:595677/1‑90 (MQ=255)
                                                                   aCTGGCGGTTGGTTGGTCGGGGAGGGGAATTATCAGCGATGGATTACTGCACAACACCCTGCGGAAATTCCTCTGGATCAAAAACTCAcc                    <  2:314820/90‑1 (MQ=255)
                                                                     tGGCGGTTGGTTGGTCGGGGAGGGGAATTATCAGCGATGGGTTACTGCACAACACCCTGCGGAAAATCCTCTGGGTCAAAAAcccaccca                  >  2:369595/1‑90 (MQ=255)
                                                                     tGGCGGTTGGGTTGTCGGGGGGGGGGATTTTCAGCGATGGGTTACTGCACAAAACCCTGCGGGAAATTCTCTGGGTCAAAAACTCACCCa                  >  2:599202/1‑90 (MQ=255)
                                                                     tGGCGGTTGGGTGGGGGGGGGGGGGGATTTTTCGCGGTGGGTTACTGCACAACACCCCTCGGGAAATTCTCTGGGGCCAAAAATCACCCa                  >  1:434349/1‑90 (MQ=255)
                                                                             ggttggtCGGGGAGGGGAATTATCAGCGATGGATTACTGCACAACACCCTGCGGAAATTCCTCTGGATCAAAAACTCACCCATTACGAAc          <  1:409005/90‑1 (MQ=255)
                                                                                tggtCGGGGAGGGGAATTATCAGCGATGGATTACTGCACAACACCCTGCGGAAATTCCTCTGGATCAAAAACTCACCCATTACGAACAGc       <  1:450659/90‑1 (MQ=255)
                                                                                     ggggaggggaATTATCAGCGATGGATTACTGCACAACACCCTGCGGAAATTCCTCTGGATCAAAAACTCACCCATTACGAACAGCTGGCa  <  2:434349/90‑1 (MQ=255)
                                                                                         |                                                                                     
TGATGATATACGTCTCTGGCAGGAAGAAGATGTGCTCTACGCCCTGACCGTATTTAACGGTGAATATACTGGCGGTTGGTTGGTCGGGGAGGGGAATTATCAGCGATGGATTACTGCACAACACCCTGCGGAAATTCCTCTGGATCAAAAACTCACCCATTACGAACAGCTGGCA  >  NZ_CP009273/4611978‑4612152

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 6 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑