Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,498,073	0	A	G	60.3%	32.2 / 72.3	58	K54E (AAA→GAA)	insQ	RNA‑guided endonuclease TnpB family protein
Reads supporting (aligned to +/- strand):  ref base A (10/13);  new base G (19/16);  total (29/29)
Fisher's exact test for biased strand distribution p-value = 5.92e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.74e-01
Rejected as consensus: Frequency below/above cutoff threshold.

ATTCCAGTTAAGACCCGGTGGTCAACAGGAGTGTGAAATGAGGCGCTTCGCAGGCGCATGTCGTTTCGTTTTCAATCGTGCTCTGGCACGTCAGAATGAGAATCATGAGGCCGGTAAT‑AAATACATCCCTTACGGGAAAATGGCTTCCTGGCTGGTTGAGTGGAAAAATGCCACTGAAACGCAATGGCTTAAAGATTCTCCCTCACAGCCATTGCAACAGTCACTGAAAGACCTTGAGCGGGCTTACAAAAACTTCTTCCGGAAGCGGGCTGCTT  >  NZ_CP009273/1497937‑1498211                                                                                                                                          |                                                                                                                                           aTTCCAGTTAAGACCCGGTGGTCAACAGGAGTGTGAAATGAGGCGCTTCGCAGGCGCATGTCGTTTCGTTTTCAATCGTGCTCTGGCACGTCAGAATGAGAATCATGAGGCCGGTAAT‑AAATACATCCCTTACGGGaaa                                                                                                                                          <  2:117779/139‑1 (MQ=255)   tCCAGTTAAGACCCGGTGGTCAACAGGAGTGTGAAATGAGGCGCTTCGCAGGCGCATGTCGTTTCGTTTTCAATCGTGCTCTGGCACGTCAGAATGAGAATCATGAGGCCGGTAAT‑AAATACATCCCTTACGGGGAAAt                                                                                                                                        >  2:749154/1‑139 (MQ=255)    ccAGTTAAGACCCGGTGGTCAACAGGAGTGTGAAATGAGGCGCTTCGCAGGCGCATGTCGTTTCGTTTTCAATCGTGCTCTGGCACGTCAGAATGAGAATCATGAGGCCGGTAAT‑AAATACATCCCTTACGGGGAAAt                                                                                                                                        <  2:106101/138‑1 (MQ=255)    ccAGTTAAGACCCGGTGGACAACAGGAGTGTGAAATGAGGCGCTTCGCAGGCGCATGTCGTTTCGTTTTCAATCGTGCTCTGGCACGTCAGAATGAGAATCATGAGGCCGGTAAT‑AAATACATCCCTTACGGGGAAAt                                                                                                                                        <  1:492003/138‑1 (MQ=255)       gTTAAGACCCGGTGGTCAACAGGAGTGTGAAATGAGGCGCTTCGCAGGCGCATGTCGTTTCGTTTTCAATCGTGCTCTGGCACGTCAGAATGAGAATCATGAGGCCGGTAAT‑AAATACATCCCTTACGGGAAAATGGCt                                                                                                                                    >  1:682173/1‑139 (MQ=255)                                  tgAAATGAGGCGCTTCGCAGGCGCATGTCGTTTCGTTTTCAATCGTGCTCTGGCACGTCAGAATGAGAATCATGAGGCCGGTAAT‑AAATACATCCCTTACGGGAAAATGGCTTCCTGGCTGGTTGAGTGGAAAAATGc                                                                                                          >  1:975462/1‑138 (MQ=255)                                    aaaTGAGGCGCTTCGCAGGCGCATGTCGTTTCGTTTTCAATCGTGCTCTGGCACGTCAGAATGAGAATCATGAGGCCGGTAATAAAATACATCCCTTACGGGGAAATGGCTTCCTGGCTGGTTGAGTGGAAAAATGCCa                                                                                                        >  2:130502/1‑139 (MQ=255)                                    aaaTGAGGCGCTTCGCAGGCGCATGTCGTTTCGTTTTCAATCGTGCTCTGGCACGTCAGAATGAGAATCATGAGGCCGGTAAT‑AAATACATCCCTTACGGGGAAATGGCTTCCTGGCTGGTTGAGTGGAAAAATGCAAc                                                                                                       >  2:339575/1‑139 (MQ=255)                                    aaaTGAGGCGCTTCGCAGGCGCATGTCGTTTCGTTTTCAATCGTGCTCTGGCACGTCAGAATGAGAATCATGAGGCCGGTAAT‑AAATACATCCCTTACGGGAAAATGGCTTCCTGGCTGGTTGAGTGGAAAAATGCCAc                                                                                                       <  1:526463/139‑1 (MQ=255)                                         aGGCGCTTCGCAGGCGCATGTCGTTTCGTTTTCAATCGTGCTCTGGCACGTCAGAATGAGAATCATGAGGCCGGTAAT‑AAATACATCCCTTACGGGAAAATGGCTTCCTGGCTGGTTGAGTGGAAAAATGCCACTGaa                                                                                                   <  1:892292/138‑1 (MQ=255)                                          ggCGCTTCGCAGGCGCATGTCGTTTCGTTTTCAATCGTGCTCTGGCACGTCAGAATGAGAATCATGAGGCCGGTAAT‑AAATACATCCCTTACGGGGAAATGGCTTCCTGGCTGGTTGAGTGGAAAAATGCCACTGAAAc                                                                                                 >  1:527811/1‑139 (MQ=255)                                             gcTTCGCAGGCGCATGTCGTTTCGTTTTCAATCGTGCTCTGGCACGTCAGAATGAGAATCATGAGGCCGGTAAT‑AAATACATCCCTTACGGGAAAATGGCTTCCTGGCTGGTTGAGTGGAAAAATGCCACTGAAACGCa                                                                                              <  2:975462/139‑1 (MQ=255)                                             gcTTCGCAGGCGCATGTCGTTTCGTTTTCAATCGTGCTCTGGCACGTCAGAATGAGAATCATGAGGCCGGTAAT‑AAATACATCCCTTACGGGAAAATGGCTTCCTGGCTGGTTGAGTGGAAAAATGCCACTGAAACGCa                                                                                              <  2:682173/139‑1 (MQ=255)                                             gcTTCGCAGGCGCATGTCGTTTCGTTTTCAATCGTGCTCTGGCACGTCAGAATGAGAATCATGAGGCCGGTAAT‑AAATACATCCCTTACGGGAAAATGGCTTCCTGGCTGGTTGAGTGGAAAAATGCCACTGAAACGCa                                                                                              <  2:282903/139‑1 (MQ=255)                                                      gcgcATGTCGTTTCGTTTTCAATCGTGCTCTGGCACGTCAGAATGAGAATCATGAGGCCGGTAAT‑AAATACATCCCTTACGGGGAAATGGCTTCCTGGCTGGTTGAGTGGAAAAATGCCACTGAAACGCAATGGCTTa                                                                                      >  1:712837/1‑138 (MQ=255)                                                         cATGTCGTTTCGTTTTCAATCGTGCTCTGGCACGTCAGAATGAGAATCATGAGGCCGGTAAT‑AAATACATCCCTTACGGGGAAATGGCTTCCTGGCTGGTTGAGTGGAAAAATGCCACTGAAACGCAATGGCTTAAAGa                                                                                  <  2:712837/139‑1 (MQ=255)                                                         cATGTCGTTTCGTTTTCAATCGTGCTCTGGCACGTCAGAATGAGAATCATGAGGCCGGTAAT‑AAATACATCCCTTACGGGGAAATGGCTTCCTGGCTGGTTGAGTGGAAAAATGCCACTGAAACGCAATGGCTTAAAGa                                                                                  <  2:761527/139‑1 (MQ=255)                                                         cATGTCGTTTCGTTTTCAATCGTGCTCTGGCACGTCAGAATGAGAATCATGAGGCCGGTAAT‑AAATACATCCCTTACGGGAAAATGGCTTCCTGGCTGGTTGAGTGGAAAAATGCCACTGAAACGCAATGGCTTAAAGa                                                                                  <  2:1009819/139‑1 (MQ=255)                                                             tcgtttcgttTTCAATCGTGCTCTGGCACGTCAGAATGAGAATCATGAGGCCGGTAAT‑AAATACATCCCTTACGGGGAAATGGCTTCCTGGCTGGTTGAGTGGAAAAATGCCACTGAAACGCAATGGCTTAAAGATtct                                                                              <  1:29353/139‑1 (MQ=255)                                                                tttcgtttTCAATCGTGCTCTGGCACGTCAGAATGAGAATCATGAGGCCGGTAAT‑AAATACATCCCTTACGGGAAAATGGCTTCCTGGCTGGTTGAGTGGAAAAATGCCACTGAAACGCAATGGCTTAAAGATTCTccc                                                                           >  2:358976/1‑139 (MQ=255)                                                                     ttttCAATCGTGCTCTGGCACGTCAGAATGAGAATCATGAGGCCGGTAAT‑AAATACATCCCTTACGGGGAAATGGCTTCCTGGCTGGTTGAGTGGAAAAATGCCACTGAAACGCAATGGCTTAAAGATTCTCCCTcaca                                                                      <  2:174990/139‑1 (MQ=255)                                                                               tGCTCTGGCACGTCAGAATGAGAATCATGAGGCCGGTAAT‑AAATACATCCCTTACGGGGAAATGGCTTCCTGGCTGGTTGAGTGGAAAAATGCCACTGAAACGCAATGGCTTAAAGATTCTCCCTCACAGCCATTGCaa                                                            <  1:339575/139‑1 (MQ=255)                                                                               tGCTCTGGCACGTCAGAATGAGAATCATGAGGCCGGTAAT‑AAATACATCCCTTACGGGAAAATGGCTTCCTGGCTGGTTGAGTGGAAAAATGCCACTGAAACGCAATGGCTTAAAGATTCTCCCTCACAGCCATTGCaa                                                            <  1:797964/139‑1 (MQ=255)                                                                                 ctctGGCACGTCAGAATGAGAATCATGAGGTCGGTAAT‑AAATACATCCCTTACGGGAAAATGGCTTCCTGGCTGGTTGAGTGGAAAAATGCCACTGAAACGCAATGGCTTAAAGATTCTCCCTCACAGCCATTGCAACa                                                          <  2:1043061/139‑1 (MQ=255)                                                                                 ctctGGCACGTCAGAATGAGAATCATGAGGCCGGTAAT‑AAATACATCCCTTACGGGAAAATGGCTTCCTGGCTGGTTGAGTGGAAAAATGCCACTGAAACGCAATGGCTTAAAGATTCTCCCTCACAGCCATTGCAACa                                                          <  1:597740/139‑1 (MQ=255)                                                                                      gCACGTCAGAATGAGAATCATGAGGCCGGTAAT‑AAATACATCCCTTACGGGGAAATGGCTTCCTGGCTGGTTGAGTGGAAAAATGCCACTGAAACGCAATGGCTTAAAGATTCTCCCTCACAGCCATTGCAACAGTCAc                                                     >  2:767311/1‑139 (MQ=255)                                                                                         cGTCAGAATGAGAATCATGAGGCCGGTAAT‑AAATACATCCCTTACGGGAAAATGGCTTCCTGGCTGGTTGAGTGGAAAAATGCCACTGAAACGCAATGGCTTAAAGATTCTCCCTCACAGCCATTGCAACAGTCACTGa                                                  <  2:32424/139‑1 (MQ=255)                                                                                          gTCAGAATGAGAATCATGAGGCCGGTAAT‑AAATACATCCCTTACGGGGAAATGGCTTCCTGGCTGGTTGAGTGGAAAAATGCCACTGAAACGCAATGGCTTAAAGATTCTCCCTCACAGCCATTGCAACAGTCACTGa                                                  >  2:488763/1‑138 (MQ=255)                                                                                           tCAGCATGAGAATCATGAGGCCGGTAAT‑AAATACATCCCTTACGGGGAAATGGCTTCCTGGCTGGTTGAGTGGAAAAATGCCACTGAAACGCa                                                                                              >  1:499670/1‑93 (MQ=255)                                                                                           tCAGAATGAGAATCATGAGGCCGGTAAT‑AAATACATCCCTTACGGGGAAATGGCTTCCTGGCTGGTTGAGTGGAAAAATGCCACTGAAACGCa                                                                                              <  2:499670/93‑1 (MQ=255)                                                                                                    gaATCATGAGGCCGGTAAT‑AAATACATCCCTTACGGGGAAATGGCTTCCTGGCTGGTTGAGTGGAAAAATGCCACTGAAACGCAATGGCTTAAAGATTCTCCCTCACAGCCATTGCAACAGTCACTGAAAGACCTTGAg                                       <  2:1288284/139‑1 (MQ=255)                                                                                                    gaATCATGAGGCCGGTAAT‑AAATACATCCCTTACGGGAAAATGGCTTCCTGGCTGGTTGAGTGGAAAAATGCCACTGAAACGCAATGGCTTAAAGATTCTCCCTCACAGCCATTGCAACAGTCACTGAAAGACCTTGAg                                       <  2:667830/139‑1 (MQ=255)                                                                                                    gaATCATGAGGCCGGTAAT‑AAATACATCCCTTACGGGAAAATGGCTTCCTGGCTGGTTGAGTGGAAAAATGCCACTGAAACGCAATGGCTTAAAGATTCTCCCTCACAGCCATTGCAACAGTCACTGAAAGACCTTGAg                                       >  1:667830/1‑139 (MQ=255)                                                                                                    gaATCATGAGGCCGGTAAT‑AAATACATCCCTTACGGGAAAATGGCTTCCTGGCTGGTTGAGTGGAAAAATGCCACTGAAACGCAATGGCTTAAAGATTCTCCCTCACAGCCATTGCAACAGTCACTGAAAGACCTTGAg                                       >  1:602393/1‑139 (MQ=255)                                                                                                     aaTCATGAGGCCGGTAAT‑AAATACATCCCTTACGGGGAAATGGCTTCCTGGCTGGTTGAGTGGAAAAATGCCACTGAAACGCAATGGCTTAAAGATTCTCCCTCACAGCCATTGCAACAGTCACTGAAAGACCTTGAGc                                      >  1:1225797/1‑139 (MQ=255)                                                                                                         aTGAGGCCGGTAAT‑AAATACATCCCTTACGGGGAAATGGCTTCCTGGCTGGTTGAGTGGAAAAATGCCACTGAAACGCAATGGCTTAAAGATTCTCCCTCACAGCCATTGCaa                                                            <  2:1261992/113‑1 (MQ=255)                                                                                                         aTGAGGCCGGTAAT‑AAATACATCCCTTACGGGGAAATGGCTTCCTGGCTGGTTGAGTGGAAAAATGCCACTGAAACGCAATGGCTTAAAGATTCTCCCTCACAGCCATTGCaa                                                            >  1:1261992/1‑113 (MQ=255)                                                                                                         aTGAGGCCGGTAAT‑AAATACATCCCTTACGGGAAAATGGCTTCCTGGCTGGTTGAGTGGAAAAATGCCACTGAAACGCAATGGCTTAAAGATTCTCCCTCACAGCCATTGCAACAGTCACTGAAAGACCTTGAGCGGGc                                  >  2:1171340/1‑139 (MQ=255)                                                                                                            aGGCCGGTAAT‑AAATACATCCCTTACGGGGAAATGGCTTCCTGGCTGGTTGAGTGGAAAAATGCCACTGAAACGCAATGGCTTAAAGATTCTCCCTCACAGCCATTGCAACAGTCa                                                      >  2:444270/1‑116 (MQ=255)                                                                                                            aGGCCGGTAAT‑AAATACATCCCTTACGGGGAAATGGCTTCCTGGCTGGTTGAGTGGAAAAATGCCACTGAAACGCAATGGCTTAAAGATTCTCCCTCACAGCCATTGCAACAGTCa                                                      <  1:444270/116‑1 (MQ=255)                                                                                                                  gTAAT‑AAATACATCCCTTACGGGGAAATGGCTTCCTGGCTGGTTGAGTGGAAAAATGCCACTGAAACGCAATGGCTTAAAGAtt                                                                                >  2:232913/1‑84 (MQ=255)                                                                                                                  gTAAT‑AAATACATCCCTTACGGGGAAATGGCTTCCTGGCTGGTTGAGTGGAAAAATGCCACTGAAACGCAATGGCTTAAAGAtt                                                                                <  1:232913/84‑1 (MQ=255)                                                                                                                     at‑aaataCATCCCTTACGGGGAAATGGCTTCCTGGCTGGTTGAGTGGAAAAATGCCACTGAAACGCAATGGCTTAAAGATTCTCCCTCACAGCCATTGCAACAGTCACTGAAAGACCTTGAGCGGGCTTACAAAAAct                       <  1:749154/138‑1 (MQ=255)                                                                                                                              aTCCCTTACGGGGAAATGGCTTCCTGGCTGGTTGAGTGGAAAAATGCCACTGAAACGCAATGGCTTAAAGATTCTCCCTcaca                                                                      <  2:282094/83‑1 (MQ=255)                                                                                                                              aTCCCTTACGGGGAAATGGCTTCCTGGCTGGTTGAGTGGAAAAATGCCACTGAAACGCAATGGCTTAAAGATTCTCCCTcaca                                                                      >  1:282094/1‑83 (MQ=255)                                                                                                                              aTCCCTTACGGGGAAATGGCTTCCTGGCTGGTTGAGTGGAAAAATGCCACTGAAACGCAATGGCTTAAAGATTCTCCCTCACAGCCATTGCAACAGTCACTGAAAGACCTTGAGCGGGCTTACAAAAACTTCTTCCgg               >  1:1274487/1‑138 (MQ=255)                                                                                                                              aTCCCTTACGGGGAAATGGCTTCCTGGCTGGTTGAGTGGAAAAATGCCACTGAAACGCAATGGCTTAAAGATTCTCCCTCACAGCCATTGCAACAGTCACTGAAAGACCTTGAGCGGGCTTACAAAAACTTCTTCCgg               >  2:786094/1‑138 (MQ=255)                                                                                                                              aTCCCTTACGGGAAAATGGCTTCCTGGCTGGTTGAGTGGAAAAATGCCACTGAAACGCAATGGCTTAAAGATTCTCCCTCACAGCCATTGCAACa                                                          >  2:204109/1‑95 (MQ=255)                                                                                                                              aTCCCTTACGGGAAAATGGCTTCCTGGCTGGTTGAGTGGAAAAATGCCACTGAAACGCAATGGCTTAAAGATTCTCCCTCACAGCCATTGCAACa                                                          <  1:204109/95‑1 (MQ=255)                                                                                                                              aTCCCTTACGGGAAAATGGCTTCCTGGCTGGTTGAGTGGAAAAATGCCACTGAAACGCAATGGCTTAAAGATTCTCCCTCACAGCCATTGCAACAGTCACTGaaa                                                >  2:632905/1‑105 (MQ=255)                                                                                                                              aTCCCTTACGGGAAAATGGCTTCCTGGCTGGTTGAGTGGAAAAATGCCACTGAAACGCAATGGCTTAAAGATTCTCCCTCACAGCCATTGCAACAGTCACTGaaa                                                <  1:632905/105‑1 (MQ=255)                                                                                                                              aTCCCTTACGGGAAAATGGCTTCCTGGCTGGTTGAGTGGAAAAATGCCACTGAAACGCAATGGCTTAAAGATTCTCCCTCACAGCCATTGCAACAGTCACTGAAAGACCTTGAGCGGGCTTACAAAAACTTCTTCCgg               >  1:502909/1‑138 (MQ=255)                                                                                                                                cccTTACGGGAAAATGGCTTCCTGGCTGGTTGAGTGGAAAAATGCCACTGAAACGCAATGGCTTAAAGATTCTCCCTCACAGCCATTGCAACAGTCACTGAAAGACCTTGAGCGGGCTTACAAAAACTTCTTCCGGAAg            >  2:746510/1‑139 (MQ=255)                                                                                                                                   ttACGGGGAAATGGCTTCCTGGCTGGTTGAGTGGAAAAATGCCACTGAAACGCAATGGCTTAAAGATTCTCCCTCACAGCCATTGCAACAGTCACTGAAAGACCTTGAGCGGGCTTACAAAAACTTCTTCCGGAAGCgg         >  2:85250/1‑139 (MQ=255)                                                                                                                                    tACGGGGAAATGGCTTCCTGGCTGGTTGAGTGGAAAAATGCCACTGAAACGCAAt                                                                                            <  1:826481/55‑1 (MQ=255)                                                                                                                                    tACGGGGAAATGGCTTCCTGGCTGGTTGAGTGGAAAAATGCCACTGAAACGCAAt                                                                                            >  2:826481/1‑55 (MQ=255)                                                                                                                                     aCGGGGAAATGGCTTCCTGGCTGGTTGAGTGGAAAAATGCCACTGAAACGCa                                                                                              >  2:588502/1‑52 (MQ=255)                                                                                                                                     aCGGGGAAATGGCTTCCTGGCTGGTTGAGTGGAAAAATGCCACTGAAACGCa                                                                                              <  1:588502/52‑1 (MQ=255)                                                                                                                                     aCGGGGAAATGGCTTCCTGGCTGGTTGAGTGGAAAAATGCCACTGAAACGCAATGGCTTAAAGATTCTCCCTCACAGCCATTGCAACAGTCACTGAAAGACCTTGAGCGGGCTTACAAAAACTTCTTCCGGAAGCGGgc       >  1:1185445/1‑139 (MQ=255)                                                                                                                                          aaaaTGGCTTCCTGGCTGGTTGAGTGGAAAAATGCCACTGAAACGCAATGGCTTAAAGATTCTCCCTCACAGCCATTGCAACAGTCACTGAAAGACCTTGAGCGGGCTTACAAAAACTTCTTCCGGAAGCGGGCTGCtt  >  2:907177/1‑139 (MQ=255)                                                                                                                                          aaaaTGGCTTCCTGGCTGGTTGAGTGGAAAAATGCCACTGAAACGCAATGGCTTAAAGATTCTCCCTCACAGCCATTGCAACAGTCACTGAAAGACCTTGAGCGGGCTTACAAAAACTTCTTCCGGAAGCGGGCTGCtt  >  1:582233/1‑139 (MQ=255)                                                                                                                                          |                                                                                                                                           ATTCCAGTTAAGACCCGGTGGTCAACAGGAGTGTGAAATGAGGCGCTTCGCAGGCGCATGTCGTTTCGTTTTCAATCGTGCTCTGGCACGTCAGAATGAGAATCATGAGGCCGGTAAT‑AAATACATCCCTTACGGGAAAATGGCTTCCTGGCTGGTTGAGTGGAAAAATGCCACTGAAACGCAATGGCTTAAAGATTCTCCCTCACAGCCATTGCAACAGTCACTGAAAGACCTTGAGCGGGCTTACAAAAACTTCTTCCGGAAGCGGGCTGCTT  >  NZ_CP009273/1497937‑1498211

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑