Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	589,934	0	T	G	41.4%	42.4 / 10.2	29	T341P (ACC→CCC)	nfrA	bacteriophage N4 receptor, outer membrane subunit
Reads supporting (aligned to +/- strand):  ref base T (2/15);  new base G (12/0);  total (14/15)
Fisher's exact test for biased strand distribution p-value = 1.75e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CAGTTGCCAGGTTAGTTGATCCAGGCGGGTAAGATTTGCCGGTTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACTGACCTTC‑TTTTAACAGCACCGGTAGCGTCGCGCCAACAACATACTGGC‑GGTTGTCGGCAAACTGTACCGTATAATTCGCCAACGCCTGAACGGGGTTAGCGCTGTATTTAGAT  >  NC_000913/589788‑590076                                                                                                                                                   |                                                                                                                                                 cAGTTGCCAGGTTAGTTGATCCAGGCGGGTAAGATTTGCCGGTTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCg                                                                                                                                              <  1:439014/151‑1 (MQ=255)          ggTTAGTTGATCCAGGCGGGGAAGATTTGCCGGTTCTTGCTGATACAGCCATCGTGCCAGACGCAGAGGTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGgggggggggggggggggggct                                                                                                                                     >  2:621146/1‑140 (MQ=255)                 tGATCCAGGCGGGTAAGATTTGCCGGTTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGgggggggggggggggcgctttt                                                                                                                                    >  1:666297/1‑133 (MQ=255)                   aTCCAGGCGGGGAAAATTTTCCGGTTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGGCGCCACGCTGACAGCATCACGCCCCTCAAGCATTTCATTGGCGgggggggggggggggcggtttt                                                                                                                                    >  2:17636/1‑131 (MQ=255)                     ccAGGCGGGTAAGATTTGCCGGTTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGcgtc                                                                                                                          <  2:384902/151‑1 (MQ=255)                        ggCGGGTAAGATTTGCCGGTTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGcgtcgt                                                                                                                        <  1:328672/150‑1 (MQ=255)                             gTAAGATTTGCCGGTTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGGGGGGGGCGGGCAGTTTTTTCGCTGCGTCGTACt                                                                                                                     >  1:450896/1‑148 (MQ=255)                                 gATTTGCCGGTTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGGGGGGGGGGGGGAGGTTTTTTGCTGCGTCGTACTGACctt                                                                                                               >  2:482749/1‑150 (MQ=255)                                    ttGCCGGTTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACTGACcttc‑tt                                                                                                           <  2:580358/150‑1 (MQ=255)                                      gCCGGTTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGGGGGGGGGGGGGGGGTTTTGGGGGCCGCCGTACTGACCCTC‑cttt                                                                                                         >  2:599402/1‑150 (MQ=255)                                      gCCGGTTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACTGACCTTC‑tttt                                                                                                         <  2:45852/150‑1 (MQ=255)                                       ccGGTTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGGGGGGGGGGGGGAGGTTTTTTGCCGCGGCGTACTCACCTTC‑ttttt                                                                                                        >  1:513480/1‑149 (MQ=255)                                       ccGGTTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACTGACCTTC‑TTTTaa                                                                                                       <  1:176916/151‑1 (MQ=255)                                       ccGGTTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACTGACCTTC‑TTTTaa                                                                                                       <  1:85134/151‑1 (MQ=255)                                           ttCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGGGGGGGGGGGGGAGTTTTTGTGCCGCGTCGTACTGACCTTC‑TTTTTACa                                                                                                     >  1:626399/1‑149 (MQ=255)                                             cTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGGGGGGGGCGGGAAGGTTTTTTGCTGCGTCGTACTGACCCTC‑TTTTTATAGc                                                                                                   >  2:726715/1‑149 (MQ=255)                                                 cTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGGGGGGGGGGAGCAGGTTTTTCGCTGCGTCGTACCGGCCCTCTTTTTAAAAGCACggg                                                                                              >  2:298964/1‑151 (MQ=255)                                                  tGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGGGGGGGGGGAGCCGGTTTTTCGCCGCGGCGTACTGACCCTT‑TTTTTACAACAcc                                                                                                >  1:804358/1‑147 (MQ=255)                                                                 gCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGGGGGGAGCAGTTTTTTGGCTGCTCCCTACGGACCTTC‑TTTTTACAACACCGGGAGGGGCGCCCccaca                                                                              >  1:8740/1‑150 (MQ=255)                                                                     gACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGGGGGGGGGGAGCAGGTTTTTCGCTGCGTCGTACTGACCTTC‑TTTTTAAAGCACCGGGAGCGTCGCGCcaacaa                                                                             >  1:158693/1‑147 (MQ=255)                                                                                  aGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACTGACCTTC‑TTTTAACAGCACCGGTAGCGTCGCGCCAACAACATACTGGC‑GGTTGTCg                                                           <  1:136963/151‑1 (MQ=255)                                                                                          tACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCAGTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACTGACCTTC‑TTTTAACAGCACCGGTAGCGTCGCGCCAACAACATACTGGC‑GGTTGTCGGCAAACt                                                    <  2:641060/150‑1 (MQ=255)                                                                                             gggTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGGGGGGGGGGAGGAGGTTTTTCGCTGCGGCGTACTGACCTTC‑TTTTTAAAGCAACGGGAGAGCCGCGCCCACAACATAATTGC‑ggggggtgggg                                                        >  1:720670/1‑134 (MQ=255)                                                                                                  gCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACTGACCTTC‑TTTTAACAGCACCGGTAGCGTCGCGCCAACAACATACTGGC‑GGTTGTCGGCAAACTGTACCGtat                                           <  2:546161/151‑1 (MQ=255)                                                                                                  gCCACGCTGACAGCAGAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACTGACCTTC‑TTTTAACAGCACCGGTAGCGTCGCGCCAACAACATACTGGC‑GGTTGTCGGCAAACTGTACCGtat                                           <  2:820649/151‑1 (MQ=255)                                                                                                    cACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACTGACCTTC‑TTTTAACAGCACCGGTAGCGTCGCGCCAACAACATACTGGC‑GGTTGTCGGCAAACTGTACCGTATaa                                         <  1:750759/151‑1 (MQ=255)                                                                                                              gCATAACGCTCCTCAAGCATTTCATTGGCGGGGGGGGGGGGGAGCAGGTTTTTCGCTGCGGCGGACTTACCTTC‑TTTTTACAGCACCGGTAGCGGCGCGCCCACAACAAACTGGCGGGTTTTTGGCAAAACGTACCCCAAAATTccc                                    >  1:392325/1‑145 (MQ=255)                                                                                                              gCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACTGACCTTC‑TTTTAACAGCACCGGTAGCGTCGCGCCAACAACATACTGGC‑GGTTGTCGGCAAACTGTACCGTATAATTCGCCAACg                               <  1:282558/151‑1 (MQ=255)                                                                                                                  aaCGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACTGACCTTC‑TTTTAACAGCACCGGTAGCGTCGCGCCAACAACATACTGGC‑GGTTGTCGGCAAACTGCACCGTATAATTCGCCAACGCCTg                           <  1:193063/151‑1 (MQ=255)                                                                                                                                   tCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACTGACCTTC‑TTTTAACAGCACCGGTAGCGTCGCGCCAACAACATACTGGC‑GGTTGTCGGCAAACTGTACCGTATAATTCGCCAACGCCTGAACGGGGTTAGCGCTg           <  2:140029/150‑1 (MQ=255)                                                                                                                                           ggggAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACTGACCTTC‑TTTTAACAGCACCGGTAGCGTCGCGCCAACAACATACTGGC‑GGTTGTCGGGAAAACGTAACCTATAAATTGCCCAACCCTGAACGGGGGTTGCGCTTGAttt      >  1:401902/1‑147 (MQ=255)                                                                                                                                            gggAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACTGACCTTC‑TTTTAACAGCACCGGTAGCGTCGCGCCAACAACATACTGGC‑GGTTTTTTGCAAAATTTACCCGATAAATCCCCCACCCCCGCACGGGGGTTGAGCTGTAtttttat  >  2:165578/1‑146 (MQ=255)                                                                                                                                                   |                                                                                                                                                 CAGTTGCCAGGTTAGTTGATCCAGGCGGGTAAGATTTGCCGGTTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACTGACCTTC‑TTTTAACAGCACCGGTAGCGTCGCGCCAACAACATACTGGC‑GGTTGTCGGCAAACTGTACCGTATAATTCGCCAACGCCTGAACGGGGTTAGCGCTGTATTTAGAT  >  NC_000913/589788‑590076

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑