Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,452,298	0	A	C	35.7%	62.5 / 12.6	56	A24A (GCA→GCC)	PP_5556	bacteriophage lysis protein
Reads supporting (aligned to +/- strand):  ref base A (21/15);  new base C (20/0);  total (41/15)
Fisher's exact test for biased strand distribution p-value = 4.01e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

ATGGTGGTAGCAACGGTCTGGAGGATCGCAAGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCGCTGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTCGGCAAGCAGTTGGCGGAGAAGGATCGCGCGCACGGTCTGGAGCGGGAGAAGGCTGCAGCAGCAGCGCTCGAT  >  NC_002947/3452163‑3452430                                                                                                                                        |                                                                                                                                     aTGCTGGTAGCAACGGTCTCGAGGATCGCAAGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCCCAGGCGGCGACCCGGCa                                                                                                                                      >  2:594852/1‑136 (MQ=255)   ggtggtAGCAACGGTCTGGAGGATCGCAAGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCCGCGCGGGCGGCGCCCGGGCAGc                                                                                                                                    >  2:295475/1‑136 (MQ=255)        tAGCAACGGTCTGGAGGATCGCAAGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCCCTGGCGGCGCCCGGGCAGCCTggg                                                                                                                               >  2:55623/1‑136 (MQ=255)          gCAACGGTCTGGAGGATCGCAAGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCGCTGGCGGCGCCCGGGCAGCCTGGgtg                                                                                                                             >  1:144976/1‑136 (MQ=255)          gCAACGGTCTGGAGGATCGCAAGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCACCGCTGGCGGCGCCCGGGCAGCCTGGgtg                                                                                                                             >  2:524847/1‑136 (MQ=255)             aCGGTCTGGAGGATCGCAAGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCGCTGGCGGCGCCCGGGCAGCCTGGGTGTgg                                                                                                                          >  1:281067/1‑136 (MQ=255)             aCGGTCTGGAGGATCGCAAGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCGCTGGCGGCGCCCGGGCAGCCTGGGTGTgg                                                                                                                          >  1:122812/1‑136 (MQ=255)                  cgggaggaTCGCAAGGCCCTCTACACGCGTGCGCTCGTGGGGCTGCTGTGAGCGCTTGGGCCACCCGCCGGGGCGCCGGGGCGCGGCGGCTGGCCGCCTGCGCGGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGc                                                                                                                     <  2:451675/134‑1 (MQ=255)                     gaggaTCGCAAGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCGCTGGCGGCGCCCGGGCCGCCTGGGTGTGGCAGGCCac                                                                                                                  >  1:523474/1‑135 (MQ=255)                             cAAGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCCGCGCTGGCGGCGCCCGGGCCGCCGGGGTGTGGCAGGCCACCGCCtata                                                                                                          >  1:471383/1‑136 (MQ=255)                             cAAGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCCCCGCTGGCGGCGCCCCGGCCGCCGGGGTGTGGCACGCCACCCCCtata                                                                                                          >  1:636926/1‑136 (MQ=255)                             cAAGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCCCCGCTCGCGGCGCCCGCGCCGCCGGGGTGTGGCGGGCCAACCCCaata                                                                                                          >  1:570897/1‑136 (MQ=255)                             cAAGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCCCTCGCGGCGCCCCGGCAGCCTGGGTGTGGcacgcccacgccaaaa                                                                                                          >  2:451630/1‑132 (MQ=255)                              aaGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCTGCCAGCGCTGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATaa                                                                                                         >  1:537958/1‑136 (MQ=255)                              aaGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCCGCGCTGGCGGCGCCCGGGCCGCCGGGGTGTGGCAGGCCACCGccgaaaa                                                                                                         >  1:560576/1‑131 (MQ=255)                              aaGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCCGCGCTGGCGGCGCCCGGGCCGCCGGGGGGTGGGGGGCCCACGCCGATaa                                                                                                         >  1:48159/1‑136 (MQ=255)                              aaGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCGCTGGCGGCGCCCGGGCAGCCTGGGGGTGGCAGGCCAACGCCTATaa                                                                                                         >  1:573845/1‑136 (MQ=255)                                ggCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCCGCGCTGGCGGCGCCCGGGCAGCCGGGGTGTGGCAGGCCAACGCCGATaaag                                                                                                       >  1:516357/1‑134 (MQ=255)                                 ccccTCTACACGCGCGCGCTCGTGGTGCGGCTGTGAGCGCTTGGGCCACCCGCCTGGGCGCCGTGGCGCTGCTGCGGGCCGCCAGCGCGGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGgc                                                                                                      <  2:443317/135‑1 (MQ=255)                                       tACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCGCTGGCGGCGCCCCGGCAGCCTGGGTGTGGCAGGCCAACGCCGATAAGGcgccgca                                                                                                >  2:529871/1‑135 (MQ=255)                                                  gcTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCCGCGCTGGCGGCGCCCGGGCCGCCGGGGTGTGGCAGGCCACCGCCTATAAGGCGCCGGGAGCTGATCAgg                                                                                     >  1:591480/1‑136 (MQ=255)                                                  gcTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCCGCGCTGGCGGCGCCCGGGCCGCCGGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCAGATCAgg                                                                                     >  1:445234/1‑136 (MQ=255)                                                  gcTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCCGCGCTGGCGGCGCCCGGGCAGCCTGGGGGTGGCAGGCCACCGCCGATAAGGCGCCGCACGCTGATCAgg                                                                                     >  1:566647/1‑136 (MQ=255)                                                  gcTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCCGCGCTGGCGGCGCCCGGGCAGCCTCGGTGTGGCAGGCCCACGCCTATAAGGCGCAGCTCGCTGATCAgc                                                                                     >  1:14685/1‑135 (MQ=255)                                                  gcTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCCGCGCTGGCGGCGCCCCGGCAGCCTGGGTGTGGCAGGCCAACGCCTAAAAGGCGCAGCACGCTGATCAgg                                                                                     >  1:270640/1‑136 (MQ=255)                                                  gcTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCCGCGCGGGCGGCGCCCGGGCCGCCGGGGTGTGGGCGGCCCCCCCCGATAAGGCGCCGCGCGCGGATCAgg                                                                                     >  2:357676/1‑136 (MQ=255)                                                  gcTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCCGCGCGGGCGGCGCCCGGGCCGCCGGGGTGTGGGAGGCCCACCCCGATAAGGCGCAGCTCGCTGCTCAgg                                                                                     >  2:542438/1‑136 (MQ=255)                                                  gcTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCCCCGCGGGCGGCGCCCGGGCCGCCTGGGTGTGGCAGGCCAACCCCGATAAGGCGCAGCTCGCTGATCAgg                                                                                     >  2:53956/1‑136 (MQ=255)                                                  gcTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCGCTGGCGGCGCCCGGGCCGCCTGGGTGTGGCAGGCCAACGCCGATAAGGCGCAGCGCGCGGCTCAgg                                                                                     >  1:38157/1‑136 (MQ=255)                                                  gcTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCGCGGGCGGCGCCCGGGCAGCCGGGGGGTGGCAGGCCAACGCCTATAACGCGCAGCTCGCTGATCAgg                                                                                     >  1:234244/1‑136 (MQ=255)                                                  gcTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCGCAGGCGGCGCCCCGGCAGCCTGGGTGTGGCAGGCCAACCCCTATAAGGCGCAGCTCCCAGATCAgg                                                                                     >  2:107031/1‑136 (MQ=255)                                                    tCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCCGCGCGGGCGGCGCCCGGGCCGCCTGGGTGTGGCAGGCCCACGCCGATAAGGCGCAGCTCGCTGATCAGGcc                                                                                   >  1:592050/1‑136 (MQ=255)                                                    tCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCCGCGCGGGCGGCGCCCGGGCCGCCGGGGTGTGGCAGGCCAACGCCGATAAGGCGCAGCTCGCTGATCAGGcc                                                                                   >  1:418525/1‑136 (MQ=255)                                                    tCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCCCCGCTGGCGGCGCCCCGGCCGCCGGGGTGTGGCAGGCCAACGCCGATAAGGCGCAGCGCGCTGATCAGGcc                                                                                   >  2:139196/1‑136 (MQ=255)                                                    tCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCGCTGGCGGCGCCCGGGCCGCCGGGGTGTGGCAGGCCAACCCCTATAAGGCGCAGCACGCAGATAAGGcc                                                                                   >  1:634243/1‑136 (MQ=255)                                                    tCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCGCTGGCGGCGCCCGGGCCGCCAGGGTGTGGGAGGCCCCCGCCGATAAGGCGCAGCTCGCGGCTGAGGcc                                                                                   >  1:51881/1‑136 (MQ=255)                                                    tCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCCCCCCCGCAGGCGGCGCCCCGGCAGCCTGGGTGTGGCAGGCCCACGCCAAAAAGGCGCAGCACGCTGATCaagac                                                                                   >  1:429069/1‑132 (MQ=255)                                                        ggTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCTGCCAGCGCTGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATg                                                                               <  2:537958/136‑1 (MQ=255)                                                             tgcCGTGCGCGGTTGGGCCCGCCGCCTGGTGGGGGTGGCGCTGCGGCTGGCCGCGTGCGGGGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTc                                                                          <  1:312064/136‑1 (MQ=255)                                                                       gcTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCCGCGCTGGCGGCGCCCGGGCCGCCAGGGTGTGGCAGGCCAACGCCAATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTCGGCAAGCAGt                                                                >  2:345364/1‑136 (MQ=255)                                                                       gcTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCGCTGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCGATAAGGCGCAGCTCGCTGATCAGGCCGCTGGCTTCGGCAAGCAGt                                                                >  1:567155/1‑136 (MQ=255)                                                                         ttGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCGCTGGCGGCGCCCCGGCCGCCGGGGGGTGGCAGGCCCACGCCGATAAGGCGCCGCTCGCTGATCAGGCCGATGACTTCGGCCAGCAGTTg                                                              >  1:622520/1‑136 (MQ=255)                                                                                  ccgccgGGGGGCCGGGGCGCGGCGGCGGGCCGCCAGCGCGGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTCGGCAAGCAGTTGGCGGAGAAg                                                     <  2:553351/136‑1 (MQ=255)                                                                                   cGCCTGGTCGCCGTGGCGCTGCTGCTGGCCCCCCGCGCTGGGGGCGCCCGGGGCGCCAGGGTGTTGCAGGGCACACCCTATAATGCGGCGCGCGCTGAGAAGGCGGCTGACTTCGGGCAGCAGTTTGCGGGGAAgg                                                    >  2:235747/1‑136 (MQ=255)                                                                                          gggCCGGGGCGCTGCGGCGGGCCGCCTGCGGCGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTCGGCAAGCAGTTGGCGGAGAAGGATcgcgc                                             <  1:88487/134‑1 (MQ=255)                                                                                          gcggcGTGGCGGTGCTGCGGGCCGCCTGCGGTGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTCGGCAAGCAGTTGGCGGAGAAGGATcgcgc                                             <  2:122812/132‑1 (MQ=255)                                                                                          gcgcgGTGGGGCTGCTGCGGGCCGCCAGCGCTGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTCGGCAAGCAGTTGGCGGAGAAGGATcgcgc                                             <  1:179668/135‑1 (MQ=255)                                                                                          gcgcgGTGGCGCGGCTGCTGGCCGCCAGGGCTGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTCGGCAAGCAGTTGGCGGAGAAGGATcgcgc                                             <  1:543576/135‑1 (MQ=255)                                                                                           cGCCGTGGCGCTGCTGCTGGCCGCCCGCGCTGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCGATAAGGCGCCGCTCGCTGATCAGGCCGATGACTTCGGCAAGCAGTTGGCGGAGAAGGATcgcgcg                                            >  2:571334/1‑136 (MQ=255)                                                                                             gggTGGGGCTGCTGCTGGCCGCCAGCGCGGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTCGGCAAGCAGTTGGCGGAGAAGGATCGCGCGCa                                          <  1:545044/134‑1 (MQ=255)                                                                                                  gcgcTGCTGCTGGCCGCCAGCGCTGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTCGGCAAGCAGTTGGCGGAGAAGGATCGCGCGCACGGTc                                     <  2:400802/136‑1 (MQ=255)                                                                                                    ggtgctgcggGCCGCCCGCGCGGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTCGGCAAGCAGTTGGCGGAGAAGGATCGCGCGCACGGTCTg                                   <  1:139196/134‑1 (MQ=255)                                                                                                         ggcgggCCGCCCGCGCGGGCGCCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTCGGCAAGCAGTTGGCGGAGAAGGATCGCGCGCACGGTCTGGAGCg                              <  1:524847/132‑1 (MQ=255)                                                                                                                     gcgcTGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATAAGGCCGATGACTTCGGCAAGCAGTTGGGGGAGAAGGATCGCGCGCACGGTCTGGAGCGGGAGAAGGCTgc                  >  2:406047/1‑136 (MQ=255)                                                                                                                        ggggcggcGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTCGGCAAGCAGTTGGCGGAGAAGGATCGCGCGCACGGTCTGGAGCGGGAGAAGGCTgcagc               <  2:523474/134‑1 (MQ=255)                                                                                                                                    gggCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTCGGCAAGCAGTTGGCGGAGAAGGATCGCGCGCACGGTCTGGAGCGGGAGAAGGCTGCAGCAGCAGCGCTCGa   >  2:39161/1‑136 (MQ=255)                                                                                                                                     ggCAGCCTGGGTGTGGCAGGCTAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTCGGCAAGCAGTTGGCGGAGAAGGATCGCGCGCACGGTCTGGAGCGGGAGAAGGCTGCAGCAGCAGCGCTCGAt  <  1:420989/136‑1 (MQ=255)                                                                                                                                        |                                                                                                                                     ATGGTGGTAGCAACGGTCTGGAGGATCGCAAGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCGCTGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTCGGCAAGCAGTTGGCGGAGAAGGATCGCGCGCACGGTCTGGAGCGGGAGAAGGCTGCAGCAGCAGCGCTCGAT  >  NC_002947/3452163‑3452430

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑