Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP009273276,0210AG57.5% 17.5 / 64.9 47pseudogene (53/249 nt)BW25113_RS01360transposase
Reads supporting (aligned to +/- strand):  ref base A (10/10);  new base G (13/14);  total (23/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.40e-01
Rejected as consensus: Frequency below/above cutoff threshold.

CCTGAGCATCTGACTGTTCTTTATTAGTGGAAGAATCCGGACCGTACTTCTTTATCCAGGCATAAAGGCTGTGGGTGGTGATATCGAGACGTGTTGCAACGCTGGCAACAGAATAACCGAGATCAACAACCTGTTTGACTGCTTCAGTTTTAAACTCTTCGGGATAACGCTTACCGCTCATGGGCACCTCTCTTTAAGCCATTTTAAATGACTCGGAGGTGTCTGTTAAACCCGTGGCGATTCAAAATTGCGATATATACATACC  >  NZ_CP009273/275893‑276157
                                                                                                                                |                                                                                                                                        
ccTGAGCATCTGACTGTTCTTTATTAGTGGAAGAATCCGGACCGTACTTCTTTATCCAGGCATAAAGGCTGTGGGTGGTGATATCGAGACGTGTTGCAACGCTGGCAACAGAATAACCGAGATCAACAGCCTGTTTGAc                                                                                                                                <  2:361454/139‑1 (MQ=255)
    aGCATCTGACTGTTCTTTATTAGTGGAAGAATCCGGACCGTACTTCTTTATCCAGGCATAAAGGCTGTGGGTGGTGATATCGAGACGTGTTGCAACGCTGGCAACAGAATAACCGAGATCAACAACCTGTTTGACTGCt                                                                                                                            >  2:221647/1‑139 (MQ=255)
          tGACTGTTCTTTATTAGTGGAAGAATCCGGACCGTACTTCTTTATCCAGGCATAAAGGCTGTGGGTGGTGATATCGAGACGTGTTGCAACGCTGGCAACAGAATAACCGAGATCAACAACCTGTTTGACTGCTTCAGtt                                                                                                                      >  2:163542/1‑139 (MQ=255)
             cTGTTCTTTATTAGTGGAAGAATCCGGACCGTACTTCTTTATCCAGGCATAAAGGCTGTGGGTGGTGATATCGAGACGTGTTGCAACGCTGGCAACAGAATAACCGAGATCAACAGCCTGTTTGACTGCTTCAGTTTTa                                                                                                                   <  2:370387/139‑1 (MQ=255)
             cTGTTCTTTATTAGTGGAAGAATCCGGACCGTACTTCTTTATCCAGGCATAAAGGCTGTGGGTGGTGATATCGAGACGTGTTGCAACGCTGGCAACAGAATAACCGAGATCAACAACCTGTTTGACTGCTTCAGTTTTa                                                                                                                   <  1:221647/139‑1 (MQ=255)
                ttCTTTATTAGTGGAAGAATCCGGACCGTACTTCTTTATCCAGGCATAAAGGCTGTGGGTGGTGATATCGAGACGTGTTGCAACGCTGGCAACAGAATAACCGAGATCAACAGCCTGTTTGACTGCTTCAGTTTTAAAc                                                                                                                >  1:150657/1‑139 (MQ=255)
                ttCTTTATTAGTGGAAGAATCCGGACCGTACTTCTTTATCCAGGCATAAAGGCTGTGGGTGGTGATATCGAGACGTGTTGCAACGCTGGCAACAGAATAACCGAGATCAACAGCCTGTTTGACTGCTTCAGTTTTAAAc                                                                                                                >  2:337658/1‑139 (MQ=255)
                 tCTTTATTAGTGGAAGAATCCGGACCGTACTTCTTTATCCAGGCATAAAGGCTGTGGGTGGTGATATCGAGACGTGTTGCAACGCTGGCAACAGAATAACCGAGATCAACAACCTGTTTGACTGCTTCAGTTTTAAAct                                                                                                               >  2:42742/1‑139 (MQ=255)
                     tattaGTGGAAGAATCCGGACCGTACTTCTTTATCCAGGCATAAAGGCTGTGGGTGGTGATATCGAGACGTGTTGCAACGCTGGCAACAGAATAACCGAGATCAACAACCTGTTTGACTGCTTCAGTTTTAAACTCtt                                                                                                            <  2:352599/138‑1 (MQ=255)
                           tGGAAGAATCCGGACCGTACTTCTTTATCCAGGCATAAAGGCTGTGGGTGGTGATATCGAGACGTGTTGCAACGCTGGCAACAGAATAACCGAGATCAACAGCCTGTTTGACTGCTTCAGTTTTAAACTCTTCGGGATa                                                                                                     <  2:150657/139‑1 (MQ=255)
                             gaagaaTCCGGACCGTACTTCTTTATCCAGGCATAAAGGCTGTGGGTGGTGATATCGAGACGTGTTGCAACGCTGGCAACAGAATAACCGAGATCAACAGCCTGTTTGACTGCTTCAGTTTTAAACTCTTCGGGATaa                                                                                                    <  1:337658/138‑1 (MQ=255)
                                  aTCCGGACCGTACTTCTTTATCCAGGCATAAAGGCTGTGGGTGGTGATATCGAGACGTGTTGCAACGCTGGCAACAGAATAACCGAGATCAACAACCTGTTTGACTGCTTCAGTTTTAAACTCTTCGGGATAACGCTTa                                                                                              <  1:345096/139‑1 (MQ=255)
                                     cGGACCGTACTTCTTTATCCAGGCATAAAGGCTGTGGGTGGTGATATCGAGACGTGTTGCAACGCTGGCAACAGAATAACCGAGATCAACAACCTGTTTGACTGCTTCAGTTTTAAACTCTTCGGGATAACGCTTACCg                                                                                           <  1:353326/139‑1 (MQ=255)
                                            tACTTCTTTATCCAGGCATAAAGGCTGTGGGTGGTGATATCGAGACGTGTTGCAACGCTGGCAACAGAATAACCGAGATCAACAGCCTGTTTGACTGCTTCAGTTTTAAACTCTTCGGGATAACGCTTACCGCTCATgg                                                                                    >  1:143683/1‑139 (MQ=255)
                                             aCTTCTTTATCCAGGCATAAAGGCTGTGGGTGGTGATATCGAGACGTGTTGCAACGCTGGCAACAGAATAACCGAGATCAACAGCCTGTTTGACTGCTTCAGTTTTAAACTCTTCGGGATa                                                                                                     >  2:398251/1‑121 (MQ=255)
                                             aCTTCTTTATCCAGGCATAAAGGCTGTGGGTGGTGATATCGAGACGTGTTGCAACGCTGGCAACAGAATAACCGAGATCAACAGCCTGTTTGACTGCTTCAGTTTTAAACTCTTCGGGATa                                                                                                     <  1:398251/121‑1 (MQ=255)
                                                    tATCCAGGCATAAAGGCTGTGGGTGGTGATATCGAGACGTGTTGCAACGCTGGCAACAGAATAACCGAGATCAACAACCTGTTTGACTGCTTCAGTTTTAAACTCTTCGGGATAACGCTTACCGCTCATggg                                                                                   <  2:57866/132‑1 (MQ=255)
                                                    tATCCAGGCATAAAGGCTGTGGGTGGTGATATCGAGACGTGTTGCAACGCTGGCAACAGAATAACCGAGATCAACAACCTGTTTGACTGCTTCAGTTTTAAACTCTTCGGGATAACGCTTACCGCTCATggg                                                                                   >  1:57866/1‑132 (MQ=255)
                                                          ggCATAAAGGCTGTGGGTGGTGATATCGAGACGTGTTGCAACGCTGGCAACAGAATAACCGAGATCAACAACCTGTTTGACTGCTTCAGTTTTAAACTCTTCGGGATAACGCTTACCGCTCATGGGCACCTCTCttt                                                                        >  2:251552/1‑137 (MQ=255)
                                                           gCATAAAGGCTGTGGGTGGTGATATCGAGACGTGTTGCAACGCTGGCAACAGAATAACCGAGATCAACAGCCTGTTTGACTGCTTCAGTTTTAAACTCtt                                                                                                            <  1:21594/100‑1 (MQ=255)
                                                           gCATAAAGGCTGTGGGTGGTGATATCGAGACGTGTTGCAACGCTGGCAACAGAATAACCGAGATCAACAGCCTGTTTGACTGCTTCAGTTTTAAACTCtt                                                                                                            >  2:21594/1‑100 (MQ=255)
                                                           gCATAAAGGCTGTGGGTGGTGATATCGAGACGTGTTGCAACGCTGGCAACAGAATAACCGAGATCAACAGCCTGTTTGACTGCTTCAGTTTTAAACTCTTCGGGATAACGCTTAc                                                                                             >  1:425194/1‑115 (MQ=255)
                                                           gCATAAAGGCTGTGGGTGGTGATATCGAGACGTGTTGCAACGCTGGCAACAGAATAACCGAGATCAACAGCCTGTTTGACTGCTTCAGTTTTAAACTCTTCGGGATAACGCTTAc                                                                                             <  2:425194/115‑1 (MQ=255)
                                                           gCATAAAGGCTGTGGGTGGTGATATCGAGACGTGTTGCAACGCTGGCAACAGAATAACCGAGATCAACAGCCTGTTTGACTGCTTCAGTTTTAAACTCTTCGGGATAACGCTTAc                                                                                             <  1:194273/115‑1 (MQ=255)
                                                           gCATAAAGGCTGTGGGTGGTGATATCGAGACGTGTTGCAACGCTGGCAACAGAATAACCGAGATCAACAGCCTGTTTGACTGCTTCAGTTTTAAACTCTTCGGGATAACGCTTAc                                                                                             >  2:194273/1‑115 (MQ=255)
                                                                     tgtgGGTGGTGATATCGAGACGTGTTGCAACGCTGGCAACAGAATAACCGAGATCAACAGCCTGTTTGACTGCTTCAGTTTTAAACTCTTCGGGATAACGCTTACCGCTCATGGGCACCTCTCTTTAAGCCATTTTaaa                                                           >  2:326218/1‑139 (MQ=255)
                                                                     tgtgGGTGGTGATATCGAGACGTGTTGCAACGCTGGCAACAGAATAACCGAGATCAACAACCTGTTTGACTGCTTCAGTTTTAAACTCTTCGGGATAACGCTTACCGCTCATGGGCACCTCTCTTTAAGCCATTTTaaa                                                           >  1:97322/1‑139 (MQ=255)
                                                                     tgtgGGTGGTGATATCGAGACGTGTTGCAACGCTGGCAACAGAATAACCGAGATCAACAACCTGTTTGACTGCTTCAGTTTTAAACTCTTCGGGATAACGCTTACCGCTCATGGGCACCTCTCTTTAAGCCATTTTaaa                                                           >  1:241048/1‑139 (MQ=255)
                                                                      gtgggtggTGATATCGAGACGTGTTGCAACGCTGGCAACAGAATAACCGAGATCAACAACCTGTTTGACTGCTTCAGTTTTAAACTCTTCGGGATAACGCTTACCGCTCATGGGCACCTCTCTTTAAGCCATTTTAAAt                                                          >  2:219099/1‑139 (MQ=255)
                                                                       tgggtggTGATATCGAGACGTGTTGCAACGCTGGCAACAGAATAACCGAGATCAACAACCTGTTTGACTGCTTCAGTTTTAAACTCTTCGGGATAACGCTTACCGCTCATGGGCACCTCTCTTTAAGCCATTTTaaa                                                           <  2:303407/137‑1 (MQ=255)
                                                                        gggtggTGATATCGAGACGTGTTGCAACGCTGGCAACAGAATAACCGAGATCAACAGCCTGTTTGACTGCTTCAGTTTTAAACTCtt                                                                                                            <  2:314907/87‑1 (MQ=255)
                                                                        gggtggTGATATCGAGACGTGTTGCAACGCTGGCAACAGAATAACCGAGATCAACAGCCTGTTTGACTGCTTCAGTTTTAAACTCtt                                                                                                            >  1:314907/1‑87 (MQ=255)
                                                                             gtgATATCGAGACGTGTTGCAACGCTGGCAACAGAATAACCGAGATCAACAGCCTGTTTGACTGCTTCAGTTTTAAACTCTTCGGGATAACGCTTACCGCTCATGGGCACCTCTCTTTAAGCCATTTTAAATGACTCg                                                    >  2:124176/1‑138 (MQ=255)
                                                                                   tCGAGACGTGTTGCAACGCTGGCAACAGAATAACCGAGATCAACAGCCTGTTTGACTGCTTCAGTTTTAAACTCTTCGGGATAACGCTTACCGCTCATGGGCACCTCTCTTTAAGCCATTTTAAATGACTCGGAGgtgt                                             >  2:361302/1‑139 (MQ=255)
                                                                                            gtTGCAACGCTGGCAACAGAATAACCGAGATCAACAGCCTGTTTGACTGCTTCAGTTTTAAACTCtt                                                                                                            >  1:400706/1‑67 (MQ=255)
                                                                                            gtTGCAACGCTGGCAACAGAATAACCGAGATCAACAGCCTGTTTGACTGCTTCAGTTTTAAACTCtt                                                                                                            <  2:400706/67‑1 (MQ=255)
                                                                                                  aCGCTGGCAACAGAATAACCGAGATCAACAACCTGTTTGACTGCTTCAGTTTTAAACTCTTCGGGATAACGCTTACCGCTCATGGGCACCTCTCTTTAAGCCATTTTAAATGACTCGGAGGTGTCTGTTAAACCCGTgg                              <  1:219099/139‑1 (MQ=255)
                                                                                                       ggCAACAGAATAACCGAGATCAACAGCCTGTTTGACTGCTTCAGTTTTAAACTCTTCGGGATAACGCTTACCGCTCATGGGCACCACTCTTTAAGCCATTTTAAATGACTCGGAGGTGTCTGTTAAACCCGTGGCGAtt                         >  2:46333/1‑139 (MQ=255)
                                                                                                        gCAACAGAATAACCGAGATCAACAACCTGTTTGACTGCTTCAGTTTTAAACTCTTCGGGATAACGCTTACCGCTCATGGGCACCTCTCTTTAAGCCATTTTAAATGACTCGGAGGTGTCTGTTAAACCCGTGGCGAtt                         >  1:2701/1‑138 (MQ=255)
                                                                                                              gAATAACCGAGATCAACAGCCTGTTTGACTGCTTCAGTTTTAAACTCTTCGGGATAACGCTTACCGCTCATGGGCACCTCTCTTTAAGCCATTTTAAATGACTCGGAGGTGTCTGTTAAACCCGTGGCGATTCAAAAtt                  <  1:326218/139‑1 (MQ=255)
                                                                                                                 tAACCGAGATCAACAACCTGTTTGACTGCTTCAGTTTTAAACTCTTCGGGATAACGCTTACCGCTCATGGGCACCTCTCTTTAAGCCATTTTAAATGACTCGGAGGTGTCTGTTAAACCCGTGGCGATTCAAAATTGCg               <  2:97322/139‑1 (MQ=255)
                                                                                                                   aCCGAGATCAACAGTCTGTTTGACTGCTTCAGTTTTAAACTCTTCGGGATAACGCCTACCGCTCATGGGCACCTCTCTTTAAGCCATTTTAAATGACTCGGAGGTGTTTGTTAAACCCGTGGCGATTCAAAATTGCGat             <  1:163968/139‑1 (MQ=255)
                                                                                                                   aCCGAGATCAACAACCTGTTTGACTGCTTCAGTTTTAAACTCTTCGGGATAACGCTTACCGCTCATGGGCACCTCTCTTTAAGCCATTTTAAATGACTCGGAGGTGTCTGTTAAACCCGTGGCGATTCAAAATTGCGat             <  1:251552/139‑1 (MQ=255)
                                                                                                                    ccGAGATCAACAGCCTGTTTGACTGCTTCAGTTTTAAACTCTTCGGGATAACGCTTACCGCTCATGGGCACCTCTCTTTAAGCCATTTTAAATGACTCGGAGGTGTCTGTTAAACCCGTGGCGATTCAAAATTGCGata            <  1:423258/139‑1 (MQ=255)
                                                                                                                         aTCAACAGCCTGTTTGACTGCTTCAGTTTTAAACTCTTCGGGATAACGCTTACCGCTCATGGGCACCTCTCTTTAAGCCATTTTAAATGACTCGGAGGTGTCTGTTAAACCCGTGGCGATTCAAAATTGCGATATatac       <  1:370593/139‑1 (MQ=255)
                                                                                                                         aTCAACAACCTGTTTGACTGCTTCAGTTTTAAACTCTTCGGGATAACGCTTACCGCTCATGGGCACCTCTCTTTAAGCCATTTTAAATGACTCGGAGGTGTCTGTTAAACCCGTGGCGATTCAAAATTGCGAtatata        >  2:5699/1‑138 (MQ=255)
                                                                                                                         aTCAACAACCTGTTTGACTGCTTCAGTTTTAAACTCTTCGGGATAACGCTTACCGCTCATGGGCACCTCTCTTTAAGCCATTTTAAATGACTCGGAGGTGTCTGTTAAACCCGTGGCGATTCAAAATTGCGATATatac       <  1:120112/139‑1 (MQ=255)
                                                                                                                              caacCTGTTTGACTGCTTCAGTTTTAAACTCTTCGGGATAACGCTTACCGCTCATGGGCAc                                                                                <  1:223116/61‑1 (MQ=255)
                                                                                                                              caacCTGTTTGACTGCTTCAGTTTTAAACTCTTCGGGATAACGCTTACCGCTCATGGGCAc                                                                                >  2:223116/1‑61 (MQ=255)
                                                                                                                              caacCTGTTTGACTGCTTCAGTTTTAAACTCTTCGGGATAACGCTTACCGCTCATGGGCACCTCTCTTTAAGCCATTTTAAATGACTCGGAGGTGTCTGTTAAACCCGTGGCGATTCAAAATTGCGATATATACATAcc  <  1:163542/139‑1 (MQ=255)
                                                                                                                                |                                                                                                                                        
CCTGAGCATCTGACTGTTCTTTATTAGTGGAAGAATCCGGACCGTACTTCTTTATCCAGGCATAAAGGCTGTGGGTGGTGATATCGAGACGTGTTGCAACGCTGGCAACAGAATAACCGAGATCAACAACCTGTTTGACTGCTTCAGTTTTAAACTCTTCGGGATAACGCTTACCGCTCATGGGCACCTCTCTTTAAGCCATTTTAAATGACTCGGAGGTGTCTGTTAAACCCGTGGCGATTCAAAATTGCGATATATACATACC  >  NZ_CP009273/275893‑276157

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑