Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	KT2440	916,696	0	T	G	43.1%	68.3 / 14.2	58	Q516P (CAG→CCG)	ltxB	Leukotoxin export ATP‑binding protein LtxB
Reads supporting (aligned to +/- strand):  ref base T (6/27);  new base G (23/2);  total (29/29)
Fisher's exact test for biased strand distribution p-value = 2.25e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

AGGTGGGCCATGGCGATGCCGTCCAGGCTGATCTCGCCCTGCACCAGATCCATGGCCCCACCCAGCGCCTGCAGCAAGGTTGATTTGCCGGCGCCGTTGCGGCCCAGCACGGCAATGCGCTCGCCCGGCTGGATATCCAGCCGGCCAATGTTCAGCACTGGCGGGTAGTCTTCGCTGTAGCGGAAGTTGGCCTGGCGCAGGCGGTACTCGCCGTGAATGGCCGGCAGGTGCACGCGGGCTTCGCCTTCGGGGTGATCGACCGG  >  KT2440/916567‑916829                                                                                                                                  |                                                                                                                                      aGGTGGGCCATGGCGATGCCGTCCAGGCTGATCTCGCCCTGCACCAGATCCATGGCCCCCCCCAGCGCCTGCAGCAAGGTTGATTTGCCGGCGCCGTTGCGGCCCAGCACGGCCATGCGCTCGCCCGGCGGGagata                                                                                                                                >  8:200431/1‑136 (MQ=255) aGGTGGGCCATGGCGATGCCGTCCAGGCTGATCTCGCCCTGCACCAGATCCATGGCCCCACCCAGCGCCTGCAGCAAGGTTGATTTGCCGGCGCCGTTGCGGCCCAGCACGGCAATGCGCTCGCCCGGCTGGATATc                                                                                                                                <  5:351442/137‑1 (MQ=255) aGGTGGGCCATGGCGATGCCGTCCAGGCTGATCTCGCCCTGCACCAGATCCATGGCCCCACCCAGCGCCTGCAGCAAGGTTGATTTGCCGGCGCCGTTGCGGCCCAGCACGGCAATGCGCTCGCCCGGCTGGATATc                                                                                                                                <  3:239428/137‑1 (MQ=255) aGGTGGGCCATGGCGATGCCGTCCAGGCTGATCTCGCCCTGCACCAGATCCATGGCCCCACCCAGCGCCTGCAGCAAGGTTGATTTGCCGGCGCCGTTGCGGCCCAGCACGGCAATGCGCTCGCCCGGCGGGATATc                                                                                                                                >  8:206776/1‑137 (MQ=255) aGGTGGGCCATGGCGATGCCGTCCAGGCTGATCTCGCCCTGCACCAGATCCATGGCCCCACCCAGCGCCTGCAGCAAGGTTGATTTGCCGGCGCCGTTGCGGCCCAGCACGGCAATGCGCTCGCCCCGCgggtgttg                                                                                                                                >  1:272109/1‑132 (MQ=255)      ggCCATGGCGATGCCGTCCAGGCTGATCTCGCCCTGCACCAGATCCATGGCCCCACCCAGCGCCTGCAGCAAGGTTGATTTGCCGGCGCCGTTGCGGCCCAGCACGGCAATGCGCTCGCCCGGCTGGATATCCAGcc                                                                                                                           <  7:363534/137‑1 (MQ=255)        ccATGGCGATGCCGTCCAGGCTGATCTCGCCCTGCACCAGATCCATGGCCCCACCCAGCGCCTGCAGCAAGGTTGATTTGCCGGCGCCGTTGCGGCCCAGCACGGCAATGCGCTCGCCCGGCTGGATATCCAGCCgg                                                                                                                         <  3:174572/137‑1 (MQ=255)        ccATGGCGATGCCGTCCAGGCTGATCTCGCCCTGCACCAGATCCATGGCCCCACCCAGCGCCTGCAGCAAGGTTGATTTGCCGGCGCCGTTGCGGCCCAGCACGGCAATGCGCTCGCCCGGCTGGATATCCAGCCgg                                                                                                                         <  5:77253/137‑1 (MQ=255)        ccATGGCGATGCCGTCCAGGCTGATCTCGCCCTGCACCAGATCCATGGCCCCACCCAGCGCCTGCAGCAAGGTTGATTTGCCGGCGCCGTTGCGGCCCAGCACGGCAATGCGCTCGCCCGGCTGGATATCCAGCCgg                                                                                                                         <  1:353965/137‑1 (MQ=255)        ccATGGCGATGCCGTCCAGGCTGATCTCGCCCTGCACCAGATCCATGGCCCCACCCAGCGCCTGCAGCAAGGTTGATTTGCCGGCGCCGTTGCGGCCCAGCACGGCAATGCGCTCGCCCGGCTGGATATCCAGCCgg                                                                                                                         <  2:191084/137‑1 (MQ=255)         cATGGCGATGCCGTCCAGGCTGATCTCGCCCTGCACCAGATCCATGGCCCCCCCCAGCGCCTGCAGCAAGGTTGATTTGCCGGCGCCGTTGCGGCCCAGCACGGCAATGCGCTCGCCCGGGTGGGTGTGCCGCCggg                                                                                                                        >  6:72365/1‑136 (MQ=255)         cATGGCGATGCCGTCCAGGCTGATCTCGCCCTGCACCAGATCCATGGCCCCACCCAGCGCCTGCAGCAAGGTTGATTTGCCGGCGCCGTTGCGGCCCAGCACGGCAATGCGCTCGCGCCGCTGGCTATACAGCCCGc                                                                                                                        >  3:292393/1‑137 (MQ=255)         cATGGCGATGCCGTCCAGGCTGATCTCGCCCTGCACCAGATCCATGGCCCCACCCAGCGCCTGCAGCAAGGTTGATTTGCCGGCGCCGTTGCGGCCCAGCACGGCAATGCGCTCGCCCGGCGGGATATACAGCCGGc                                                                                                                        >  2:72739/1‑137 (MQ=255)             gCGATGCCGTCCAGGCTGATCTCGCCCTGCACCAGATCCATGGCCCCACCCAGCGCCTGCAGCAAGGTTGATTTGCCGGCGCCGTTGCGGCCCAGCACGGCAATGCGCTCGCCCGGCTGGATATCCAGCCGGCCAAt                                                                                                                    <  5:5678/137‑1 (MQ=255)              cGATGCCGTCCAGGCTGATCTCGCCCTGCACCAGATCCATGGCCCCACCCAGCGCCTGCAGCAAGGTTGATTTGCCGGCGCCGTTGCGGCCCAGCACGGCAATGCGCTCGCCCGGCGGGAGATCCAGCCGGCCCAtt                                                                                                                   >  8:331240/1‑136 (MQ=255)               gATGCCGTCCAGGCTGATCTCGCCCTGCACCAGATCCATGGCCCCACCCAGCGCCTGCAGCAAGGTTGATTTGCCGGCGCCGTTGCGGCCCCGCACGGCAAGGCGCTCGCCCGGCGGGTAATACCGCCCGCCAAAGt                                                                                                                  >  2:320797/1‑137 (MQ=255)               gATGCCGTCCAGGCTGATCTCGCCCTGCACCAGATCCATGGCCCCACCCAGCGCCTGCAGCAAGGTTGATTTGCCGGCGCCGTTGCGGCCCAGCACGGCAATGCGCTCGCCCGGCTGGGTATAAAGCCGGCCAATGt                                                                                                                  >  5:329960/1‑137 (MQ=255)               gATGCCGTCCAGGCTGATCTCGCCCTGCACCAGATCCATGGCCCCACCCAGCGCCTGCAGCAAGGTTGATTTGCCGGCGCCGTTGCGGCCCAGCACGGCAATGCGCTCGCCCGGCGGGATTTCCCGCCGGCCCATGt                                                                                                                  >  2:135590/1‑137 (MQ=255)                  gCCGTCCAGGCTGATCTCGCCCTGCACCAGATCCATGGCCCCACCCAGCGCCTGCAGCAAGGTTGATTTGCCGGCGCCGTTGCGGCCCAGCACGGCAATGCGCTCGCCCGGCTGGATATCCAGCCGGCCAATGTTCa                                                                                                               <  2:255144/137‑1 (MQ=255)                  caggTCCAGGCTGATCTCGCCCTGCACCAGATCCATGGCCCCACCCAGCGCCTGCAGCAAGGTTGATTTGCCGGCGCCGTTGCGGCCCAGCACGGCAATGCGCTCGCCCGGCTGGATATCCAGCCGGCCAATGTTCa                                                                                                               <  3:68996/134‑1 (MQ=255)                   ccGTCCAGGCTGATATCTAAATGAACAAGATCCATGGCCCCACCCAGCGCCTGCAGCAAGGTTGATTTGCCGGCGCCGTTGCGGCCCAGCACGGCAATGCGCTCGCGCGGCGGGGTTTACAGCCCGCGCATGttgac                                                                                                              >  3:418047/1‑134 (MQ=255)                    cGTCCAGGCTGATCTCGCCCTGCACCAGATCCATGGCCCCACCCAGCGCCTGCAGCAAGGTTGATTTGCCGGCGCCGTTGCGGCCCAGCACGGCAATGCGCTCGCCCGGCTGGATATCCAGCCGGCCAATGTTCAGc                                                                                                             <  5:21896/137‑1 (MQ=255)                         aGGCTGATCTCGCCCTGCACCAGATCCATGGCCCCACCCAGCGCCTGCAGCAAGGTTGATTTGCCGGCGCCGTTGCGGCCCCGCACGGCAATGCGCTCGCCCGGCGGGATATCCACCCGGCCCAAGTGCCGGACTgg                                                                                                        >  7:139958/1‑137 (MQ=255)                         aGGCTGATCTCGCCCTGCACCAGATCCATGGCCCCACCCAGCGCCTGCAGCAAGGTTGATTTGCCGGCGCCGTTGCGGCCCAGCACGGCAATGCGCTCGCCCGGCTGGATATCCAGCCGGCCAATGTTCAGCACTgg                                                                                                        <  2:36926/137‑1 (MQ=255)                         aGGCTGATCTCGCCCTGCACCAGATCCATGGCCCCACCCAGCGCCTGCAGCAAGGTTGATTTGCCGGCGCCGTTGCGGCCCAGCACGGCAATGCGCTCGCCCGGCGGGCTATCCAGCCGGCCCATGTTGAGCACTgg                                                                                                        >  5:111273/1‑137 (MQ=255)                          ggCTGATCTCGCCCTGCACCAGATCCATGGCCCCACCCAGCGCCTGCAGCAAGGTTGATTTGCCGGCGCCGTTGCGGCCCAGCACGGCAATGCGCTCGCCCGGCTGGATATCCAGCCGGCCAATGTTCAGCACTGGc                                                                                                       <  2:173494/137‑1 (MQ=255)                                  tcGCCCTGCACCAGATCCATGGCCCCACCCAGCGCCTGCAGCAAGGTTGATTTGCCGGCGCCGTTGCGGCCCAGCACGGCAATGCGCTCGCCCCGCGGGGTATCCAGCCCGCCCAATTTCAGCACTGGCGGGGAGtg                                                                                               >  1:45740/1‑136 (MQ=255)                                   cGCCCTGCACCAGATCCATGGCCCCACCCAGCGCCTGCAGCAAGGTTGATTTGCCGGCGCCGTTGCGGCCCAGCACGGCAATGCGCTCGCCCCGCGGGCTATCCAGCCGGCCCATGTTCAGCACTGGCGGGTAgctg                                                                                              >  4:68996/1‑134 (MQ=255)                                   cGCCCTGCACCAGATCCATGGCCCCACCCAGCGCCTGCAGCAAGGTTGATTTGCCGGCGCCGTTGCGGCCCAGCACGGCAATGCGCTCGCCCCGCGGGATATCCAGCCGGCCAATGTTCAGCACTGGCGGGTAGTCt                                                                                              >  6:351913/1‑137 (MQ=255)                                        tGCACCAGATCCATGGCCCCACCCAGCGCCTGCAGCAAGGTTGATTTGCCGGCGCCGTTGCGGCCCAGCACGGCAATGCGCTCGCCCGGCTGGATATCCAGCCCGCCAAAGTTCAGCACTGGCGGGTAGTCTTAGCt                                                                                         >  8:353553/1‑137 (MQ=255)                                        tGCACCAGATCCATGGCCCCACCCAGCGCCTGCAGCAAGGTTGATTTGCCGGCGCCGTTGCGGCCCAGCACGGCAATGCGCTCGCCCGGCGGGATATCCAGCCGGCCAATGTTCAGCACTGGCGGGTAGTCTTCGCt                                                                                         >  6:350316/1‑137 (MQ=255)                                         gCACCAGATCCATGGCCCCACCCAGCGCCTGCAGCAAGGTTGATTTGCCGGCGCCGTTGCGGCCCAGCACGGCAATGCGCTCGCCCGGCTGGATATCCAGCCGGCCAATGTTCAGCACTGGCGGGTAGTCTTCGCTg                                                                                        <  1:301467/137‑1 (MQ=255)                                            ccAGATCCATGGCCCCACCCAGCGCCTGCAGCAAGGTTGATTTGCCGGCGCCGTTGCGGCCCAGCACGGCAATGCGCTCGCCCCGCGGGCTATACAGCCGGCCCAAGTTAAGCACAGGCGGGGTGTCGTAGCTGTAg                                                                                     >  4:57431/1‑137 (MQ=255)                                             cAGATCCATGGCCCCACCCAGCGCCTGCAGCAAGGTTGATTTGCCGGCGCCGTTGCGGCCCAGCACGGCAATGCGCTCGCCCGGCTGGATATACCGCCCCGCAAAGTTCATCACGGGGGGGTTGTCTTAGCTggtgg                                                                                    >  4:50552/1‑133 (MQ=255)                                                   cATGGCCCCACCCAGCGCCTGCAGCAAGGTTGATTTGCCGGCGCCGTTGCGGCCCAGCACGGCAATGCGCTCGCCCGGCGGGGAATCCACCCGCCCAAACTTTATCAAGGGGGGGGTGTGTTCGCTGTTGCGCAAGt                                                                              >  8:49083/1‑137 (MQ=255)                                                      ggCCCCACCCAGCGCCTGCAGCAAGGTTGATTTGCCGGCGCCGTTGCGGCCCAGCACGGCAATGCGCTCGCGCGGCGGGGGATCCAGCCGGCCCATGTTGAGCACTGGCGGGTTGTGTTGGGGGTAGGGGGAGTTgg                                                                           >  5:48007/1‑137 (MQ=255)                                                       gCCCCACCCAGCGCCTGCAGCAAGGTTGATTTGCCGGCGCCGTTGCGGCCCAGCACGGCAATGCGCTCGCCCCGCGGGGAATAAAGCCCGCCAATTTTAAGCACTGGCGGGTAGTCTTAGCTGTAGCGGAAGTTggg                                                                          >  6:127098/1‑136 (MQ=255)                                                           cacccaGCGCCTGCAGCAAGGTTGATTTGCCGGCGCCGTTGCGGCCCAGCACGGCAATGCGCTCGCCCGGCTGGATATCCAGCCGGCCAATGTTCAGCACTGGCGGGTAGTCTTCGCTGTAGCGGAAGTTGGCCTgg                                                                      <  5:431814/137‑1 (MQ=255)                                                             cccaGCGCCTGCAGCAAGGTTGATTTGCCGGCGCCGTTGCGGCCCAGCACGGCAATGCGCTCGCGCGCCGGGGTATGAAGCCCGGCAAAGTTAATCACACGCGGGGATTAATCGCTGTGGCGCGAGTTGGCCggggg                                                                    >  4:215709/1‑135 (MQ=255)                                                               caGCGCCTGCAGCAAGGTTGATTTGCCGGCGCCGTTGCGGCCCAGCACGGCAATGCGCTCGCCCGGCTGGATATCCAGCCGTCCAATGTTCAGCACTGGCGGGTAGTCt                                                                                              <  2:405925/109‑1 (MQ=255)                                                               caGCGCCTGCAGCAAGGTTGATTTGCCGGCGCCGTTGCGGCCCAGCACGGCAATGCGCTCGCCCGGCTGGATATCCAGCCGCCCAATGTTCAGCACTGGCGGGTAGTCt                                                                                              >  1:405925/1‑109 (MQ=255)                                                                         agcaAGGTTGATTTGCCGGCGCCGTTGCGGCCCAGCACGGCAATGCGCTCGCCCGGCGGGATATCCAGCCGGCCAATGTTGAGCCCGGGCGGGGAGTCTTCGCTGTTGCGGAAGTTGGCCTGGCGCCGGCGGTACTc                                                        >  7:435830/1‑137 (MQ=255)                                                                              ggTTGATTTGCCGGCGCCGTTGCGGCCCAGCACGGCAATGCGCTCGCCCGGCTGGATATCCAGCCGGCCAATGTTCAGCACTGGCGGGTAGTCTTCGCTGTAGCGGAAGTTGGCCTGGCGCAGGCGGTACTCGCCGt                                                   <  3:341324/137‑1 (MQ=255)                                                                                      tGCCGGCGCCGTTGCGGCCCAGCACGGCAATGCGCTCGCCCGGCGGGGTATCCCGCCCGCCCATGGTTAGCACTGGGGGGGTGTCTTCGGTGGTGCGGGAGGTTGGCGGGGGCCGGGGGGTCTCGCCGTGCATGGcc                                           >  6:311963/1‑137 (MQ=255)                                                                                      tGCCGGCGCCGTTGCGGCCCAGCACGGCAATGCGCTCGCCCGGCGGGGTATACACCCGGCCAATGGTGAGCACGGGCGGGTAGTCTTGGCGGTAGCGGAAGTTGGCCGGGCGCAGGCGGTAATCGGCGGGATTGGcc                                           >  4:92404/1‑137 (MQ=255)                                                                                               cGTTGCGGCCCAGCACGGCAATGCGCTCGCCCGGCTGGATATCCAGCCGGCCAATGTTCAGCACTGGCGGGTAGTCTTCGCTGTAGCGGAAGTTGGCCTGGCGCAGGCGGTACTCGCCGTGAATGGCCGGCAGGTGc                                  <  4:89786/137‑1 (MQ=255)                                                                                                      gCCCTGCTCTGCTATGCGCTGGCCGGGCGGTATATCGAGCCGGCCAATGTTCAGCACTGGCGGGTAGTCTTCGCTGTAGCGGAAGTTGGCCTGGCGCAGGCGGTACTCGCCTTGAATGGCCGGCAGGTGCACGCggg                           <  1:452897/137‑1 (MQ=255)                                                                                                      gCCCAGCACGGCAATGCGCTCGCCCGGCTGGATATCCAGCCGGCCAATGTTCAGCACTGGCGGGTAGTCTTCGCTGTAGCGGAAGTTGGCCTGGCGCAGGCGGTACTCGCCGTGAATGGCCGGCAGGTGCACGTggg                           <  2:272109/137‑1 (MQ=255)                                                                                                      gCCCAGCACGGCAATGCGCTCGCCCGGCTGGATATCCAGCCGGCCAATGTTCAGCACTGGCGGGTAGTCTTCGCTGTAGCGGAAGTTGGCCTGGCGCAGGCGGTACTCGCCGTGAATGGCCGGCAGGTGCACGCggg                           <  7:331240/137‑1 (MQ=255)                                                                                                      gCCCAGCACGGCAATGCGCTCGCCCGGCTGGATATCCAGCCGGCCAATGTTCAGCACTGGCGGGTAGTCTTCGCTGTAGCGGAAGTTGGCCTGGCGCAGGCGGTACTCGCCGTGAATGGCCGGCAGGTGCACGCggg                           <  2:266294/137‑1 (MQ=255)                                                                                                          aGCACGGCAATGCGCTCGCCCGGCTGGATATCCAGCCGGCCAATGTTCAGCTCTGGCGGGTAGTCTTCGCTGTAGCGGAAGTTGGCCTGGCGCAGGCGGTACTCGCCGTGAATGGCCGGCAGGTGCACGCGGGCTTc                       <  8:160350/137‑1 (MQ=255)                                                                                                                    tGCGCTCGCCCCGCGGGGAATCCAGCCGGCCAATGTTCAGCACTGGCGGGTGGTCTTAGCTGTAGCGGAAGTTGGGCGGGGGCAGGCGGGTCTCGCCGTGAATGGCCGGCCGGTGCACGCGGGCGTCGCCGTCgggg             >  4:166163/1‑137 (MQ=255)                                                                                                                       gcTCGCCCGGCGGGGTATCCAGCCCGGCCATGTTCAGCACTGGCGGGTTGTCTTGGCTGTAGCGGCAGTTGGCCTGGCGCCGGCGGTACTCGCCGTGAATGGCCGGCAGGTGCACGCCGGCTTGGCCGTCGGGGTgt          >  8:126213/1‑136 (MQ=255)                                                                                                                               ggCTGTATATCCAGCCGGCCGATGTTCAGCACTGGCGGGTAGTCTTCGCTGTAGCGGAAGTTGGCCTGGCGCAGGCGGTACTCGCCGTGAATGGCCGGCAGGTGCACGCGGGCTTCGCCTTCGGGGTGATCGACCgg  <  7:130636/137‑1 (MQ=255)                                                                                                                               ggCTGGATATCCAGCCGGCCAATGTTCAGCACTGGCGGGTAGTCTTCGCTGTAGCGGAAGTTGGCCTGGCGCAGGCGGTACTCGCCGTGAATGGCCGGCAGGTGCACGCGGGCTTCGCCTTCGGGGTGATCGACCgg  <  6:422136/137‑1 (MQ=255)                                                                                                                               ggCTGGATATCCAGCCGGCCAATGTTCAGCACTGGCGGGTAGTCTTCGCTGTAGCGGAAGTTGGCCTGGCGCAGGCGGTACTCGCCGTGAATGGCCGGCAGGTGCACGCGGGCTTCGCCTTCGGGGTGATCGACCgg  <  4:190825/137‑1 (MQ=255)                                                                                                                               ggCTGGATATCCAGCCGGCCAATGTTCAGCACTGGCGGGTAGTCTTCGCTGTAGCGGAAGTTGGCCTGGCGCAGGCGGTACTCGCCGTGAATGGCCGGCAGGTGCACGCGGGCTTCGCCTTCGGGGTGATCGACCgg  <  6:100333/137‑1 (MQ=255)                                                                                                                               ggCTGGATATCCAGCCGGCCAATGTTCAGCACTGGCGGGTAGTCTTCGCTGTAGCGGAAGTTGGCCTGGCGCAGGCGGTACTCGCCGTGAATGGCCGGCAGGTGCACGCGGGCTTCGCCTTCGGGGTGATCGACCgg  <  4:437063/137‑1 (MQ=255)                                                                                                                               ggCGGGATATCCAGCCGGCCAATGTTCAGCACTGGAGGGTAGTCTTCGCTGTAGCGGAAGTTGGCCTGGCGCAGGCGGTACTCGCCTTGAATGGCCGGCAGGTGCACGCGGGCTTCGCCTTCGGGGTGATCGACCgg  <  3:6423/137‑1 (MQ=255)                                                                                                                                  |                                                                                                                                      AGGTGGGCCATGGCGATGCCGTCCAGGCTGATCTCGCCCTGCACCAGATCCATGGCCCCACCCAGCGCCTGCAGCAAGGTTGATTTGCCGGCGCCGTTGCGGCCCAGCACGGCAATGCGCTCGCCCGGCTGGATATCCAGCCGGCCAATGTTCAGCACTGGCGGGTAGTCTTCGCTGTAGCGGAAGTTGGCCTGGCGCAGGCGGTACTCGCCGTGAATGGCCGGCAGGTGCACGCGGGCTTCGCCTTCGGGGTGATCGACCGG  >  KT2440/916567‑916829

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑