Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,473,402	0	G	T	48.8%	31.9 / 34.3	43	pseudogene (2886/3497 nt)	ydbA	pseudogene, autotransporter homolog; interrupted by IS2 and IS30
Reads supporting (aligned to +/- strand):  ref base G (5/17);  new base T (21/0);  total (26/17)
Fisher's exact test for biased strand distribution p-value = 7.67e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACCGAATACGACATGCTGGCATTGCGTAAAACTATCGACCTGAGCGAAAGCCAGACGATGAGTCTGGAGTACGGTATCGCTCGTCTCGATGGTGATGGTGCGCAGAAAGCGGGTGATAATGGCGTTACAGGCGGTTATAGCCAGTTTTTTGGCCTGAAACATCAGATGTCGTTCGATAACGGCATGAACT‑GGAATAACGCCTTGCGTTACGACGTTCACAACCTTGACAGCAGCCGCTCGATTGCATTTGGCAACACGAACAAAACGGCTGATACCGACGTGAAACAGCAGTACCTGG  >  NC_000913/1473252‑1473549                                                                                                                                                       |                                                                                                                                                     aCCGAATACGACATGCTGGCATTGCGTAAAACTATCGACCTGAGCGAAAGCCAGACGATGAGTCTGGAGTACGGTATCGCTCGTCTCGATGGTGATGGTGCGCAGAAAGCGGGTGATAATGGCGTTACAGGCGGTTATAGCCAGTTTTTTg                                                                                                                                                      <  2:312178/151‑1 (MQ=255)        aCGACATGCTGGCATTGCGTAAAACTATCGACCTGAGCGAAAGCCAGACGATGAGTCTGGAGTACGGTATCGCTCGTCTCGATGGTGATGGTGCGCAGAAAGCGGGTGATAATGGCGTTACAGGCGGTTATAGCCAGTTTTTTGGCCTGa                                                                                                                                                <  2:739926/150‑1 (MQ=255)            cATGCTGGCATTGCGTAAAACTATCGACCTGAGCGAAAGCCAGACGATGAGTCTGGAGTACGGTATCGCTCGTCTCGATGGTGATGGTGCGCAGAAAGCGGGTGATAATGGCGTTACAGGCGGTTATAGCCAGTTTTTTGGCCTGAAACAt                                                                                                                                           <  1:857500/151‑1 (MQ=255)             aTGCTGGCATTGCGTAAAACTATCGACCTGAGCGAAAGCCAGACGATGAGTCTGGAGTACGGTATCGCTCGTCTCGATGGTGATGGTGCGCAGAAAGCGGGTGATAATGGCGTTACAGGCGGTTATAGCCAGTTTTTTGGCCTGAAACATc                                                                                                                                          <  1:551861/151‑1 (MQ=255)              tGCTGGCATTGCGTAAAACTATCGACCTGAGCGAAAGCCAGACGATGAGTCTGGAGTACGGTATCGCTCGTCTCGATGGTGATGGTGCGCAGAAAGCGGGTGATAATGGCGTTACAGGCGGTTATAGGCAGTTTTTTTTGCTGaaa                                                                                                                                              >  1:804331/1‑146 (MQ=255)              tGCTGGCATTGCGTAAAACTATCGACCTGAGCGAAAGCCAGACGATGAGTCTGGAGTACGGTATCGCTCGTCTCGATGGTGATGGTGCGCAGAAAGCGGGTGATAATGGCGTTACAGGCGGTTATAGACAGTGTTTTTGTCTGaaaaa                                                                                                                                            >  2:250853/1‑146 (MQ=255)                  ggCATTGCGTAAAACTATCGACCTGAGCGAAAGCCAGACGATGAGTCTGGAGTACGGTATCGCTCGTCTCGATGGTGATGGTGCGCAGAAAGCGGGTGATAATGGCGTTACAGGCGGTTATAGCCAGTTTTTTGGCCTGAAACATCAGATg                                                                                                                                     <  1:207443/151‑1 (MQ=255)                    cATTGCGTAAAACTATCGACCTGAGCGAAAGCCAGACGATGAGTCTGGAGTACGGTATCGCTCGTCTCGATGGTGATGGTGCGCAGAAAGCGGGTGATAATGGCGTTACAGGCGGTTATAGCCCGGTTTTTTGGCTGGAAAATCa                                                                                                                                         >  2:509437/1‑145 (MQ=255)                         cGTAAAACTATCGACCTGAGCGAAAGCCAGACGATGAGTCTGGAGTACGGTATCGCTCGTCTCGATGGTGATGGTGCGCAGAAAGCGGGTGATAATGGCGTTACAGGCGGATATAAACAGATTTTTTGCCTGgaaactaaaagcgtgt                                                                                                                                 >  1:203189/1‑135 (MQ=255)                          gTAAAACTATCGACCTGAGCGAAAGCCAGACGATGAGTCTGGAGTACGGTATCGCTCGTCTCGATGGTGATGGTGCGCAGAAAGCGGGTGATAATGGCGTTACAGGCGGTTTTAGCCAGTTTTTTTGCCTGGAAAATCAGAAGTCGtt                                                                                                                                >  1:690130/1‑148 (MQ=255)                            aaaaCTATCGACCTGAGCGAAAGCCAGACGATGAGTCTGGAGTACGGTATCGCTCGTCTCGATGGTGATGGTGCGCAGAAAGCGGGTGATAATGGCGTTACAGGCGGTTATAGCCAGGTTTTTTGGCTGAAAAATCAGATGTCGtt                                                                                                                                >  1:229548/1‑146 (MQ=255)                              aaCTATCGACCTGAGCGAAAGCCAGACGATGAGTCTGGAGTACGGTATCGCTCGTCTCGATGGTGATGGTGCGCAGAAAGCGGGTGATAATGGCGTTACAGGCGGTTATAGCCAGTTTTTTGGCCTGAAACATCAGATGTCGTTCGATAAc                                                                                                                         <  1:257532/151‑1 (MQ=255)                                  aTCGACCTGAGCGAAAGCCAGACGATGAGTCTGGAGTACGGTATCGCTCGTCTCGATGGTGATGGTGCGCAGAAAGCGGGTGATAATGGCGTTACAGGCGGTTATAGCCAGTTTTTTTGCCTGAAACATCAGATGTCGTTCGATAACGGc                                                                                                                      >  1:802095/1‑150 (MQ=255)                                  aTCGACCTGAGCGAAAGCCAGACGATGAGTCTGGAGTACGGTATCGCTCGTCTCGATGGTGATGGTGCGCAGAAAGCGGGTGATAATGGCGTTACAGGCGGTTATAGCCAGTTTTTTGGCCTGAAACATCAGATGTCGTTCGATAACgg                                                                                                                       <  1:690013/149‑1 (MQ=255)                                   tCGACCTGAGCGAAAGCCAGACGATGAGTCTGGAGTACGGTATCGCTCGTCTCGATGGTGATGGTGCGCAGAAAGCGGGTGATAATGGCGTTACAGGCGGTTTTAGCCAGGTTTTTTGGCTGGAACATCAAATGTCggttggtaa                                                                                                                          >  1:164848/1‑137 (MQ=255)                                    cGACCTGAGCGAAAGCCAGACGATGAGTCTGGAGTACGGTATCGCTCGTCTCGATGGTGATGGTGCGCAGAAAGCGGGTGATAATGGCGTTACAGGCGGTTATAGCCAGTTTTTTTGCCTGGAAAAACAGATGTCGTTCGGTAAAGGCAt                                                                                                                    >  1:109116/1‑150 (MQ=255)                                         tGAGCGAAAGCCAGACGATGAGTCTGGAGTACGGTATCGCTCGTCTCGATGGTGATGGTGCGCAGAAAGCGGGTGATAATGGCGTTACAGGCGGTTTTAACCCGGTTTTTTGGCTGAAACATCAGATGTCGTTCTGTAACGGCCTGaa                                                                                                                 >  1:404394/1‑148 (MQ=255)                                           aGCGAAAGCCAGACGATGAGTCTGGAGTACGGTATCGCTCGTCTCGATGGTGATGGTGCGCAGAAAGCGGGTGATAATGGCGTTACAGGCGGGTTTAGCCAGGTTTTTTGCCTGGAACAACAGATGTCGTTCGGTAAAGGCAAGGACT‑gg                                                                                                            >  2:484582/1‑150 (MQ=255)                                              gAAAGCCAGACGATGAGTCTGGAGTACGGTATCGCTCGTCTCGATGGTGATGGTGCGCAGAAAGCGGGTGATAATGGCGTTACAGGCGGTTTTAACCCGGTTTTTTGGCTGAAAAAAAAGATGTCGGTCGATAAAGGGATGAAAT‑gg                                                                                                            >  1:727716/1‑147 (MQ=255)                                              gAAAGCCAGACGATGAGTCTGGAGTACGGTATCGCTCGTCTCGATGGTGATGGTGCGCAGAAAGCGGGTGATAATGGCGTTACAGGCGGTTATAGCCCGGTTTTTTTGCTGGAACATCAGATGGCGTTCGGTAACgg                                                                                                                       >  2:541702/1‑137 (MQ=255)                                              gAAAGCCAGACGATGAGTCTGGAGTACGGTATCGCTCGTCTCGATGGTGATGGTGCGCAGAAAGCGGGTGATAATGGCGTTACAGGCGGTTATAGCCAGGTTTTTTGGCTGGAAAATCAGATGTCGTTTGATAACGGCATGAAAT‑ggga                                                                                                          >  2:499586/1‑147 (MQ=255)                                              gAAAGCCAGACGATGAGTCTGGAGTACGGTATCGCTCGTCTCGATGGTGATGGTGCGCAGAAAGCGGGTGATAATGGCGTTACAGGCGGTTATAGACCGATTTTTTTGCTGAAACATAAAATATAGTTTCATAACAGGATGAACtcg                                                                                                             >  2:430092/1‑145 (MQ=255)                                               aaaGCCAGACGATGAGTCTGGAGTACGGTATCGCTCGTCTCGATGGTGATGGTGCGCAGAAAGCGGGTGATAATGGCGTTACAGGCGGTTTTTGCCCGGTTTTTTGGCTGGAACAACCCATttcgttcggttacagccgtg                                                                                                                  >  2:89402/1‑129 (MQ=255)                                                 aGCCAGACGATGAGTCTGGAGTACGGTATCGCTCGTCTCGATGGTGATGGTGCGCAGAAAGCGGGTGATAATGGCGTTACAGGCGGTTTTTACCCGTTTTTTTGCCTGAAAAATAAGAAGTCGTTTCATAACGGGATGAACA‑GGGATaa                                                                                                       >  1:212850/1‑149 (MQ=255)                                                     aGACGATGAGTCTGGAGTACGGTATCGCTCGTCTCGATGGTGATGGTGCGCAGAAAGCGGGTGATAATGGCGTTACAGGCGGTTATAAGCCGTTTTTTTGCCCGGAACAACAAATGTGGTTCGGTAAAAGCATGGACttggaaaa                                                                                                        >  2:320326/1‑138 (MQ=255)                                                      gACGATGAGTCTGGAGTACGGTATCGCTCGTCTCGATGGTGATGGTGCGCAGAAAGCGGGTGATAATGGCGTTACAGGCGGTTATAGCCAGTTTTTTGGCCTGAAACATCAGATGTCATTCGATAACGGCATGAACT‑GGAATAACGcc                                                                                                   <  2:242856/148‑1 (MQ=255)                                                                   gAGTACGGTATCGCTCGTCTCGATGGTGATGGTGCGCAGAAAGCGGGTGATAATGGCGTTACAGGCGGTTATAGCCAGTTTTTTGGCCTGAAACATCAGATGTCGTTCGATAACGGCATGAACT‑GGAATAACGCCTTGCGTTACGACGTTc                                                                                   <  1:850731/151‑1 (MQ=255)                                                                            aTCGCTCGTCTCGATGGTGATGGTGCGCAGAAAGCGGGTGATAATGGCGTTACAGGCGGTTATAGCCAGTTTTTTGGCCTGAAACATCAGATGTCGTTCGATAACGGCATGAACT‑GGAATAACGCCTTGCGTTACGACGTTCACAACCTTg                                                                          <  2:619966/151‑1 (MQ=255)                                                                                          tggtgatggtgCGCAGAAAGCGGGTGATAATGGCGTTACAGGCGGTTATAGCCCGGTTTTTTGCCTGCAAAAACAGATGTCGTTCGGTAAAGGCAAGGACT‑TGAATAAAGCCCTGCGGTTCGACGTTCACAACCTCTACAACAGCCGccc                                                             >  2:709270/1‑148 (MQ=255)                                                                                            gtgatggtgCGCAGAAAGCGGGTGATAATGGCGTTACAGGCGGTTATAGCCAGTTTTTTGGCCTGAAACATCAGATGTCGTTCGATAACGGCATGAACT‑GGAATAACGCCTTGCGTTACGACGTTCACAACCTTGACAGCAGCCGCTCGAt                                                          <  2:306429/151‑1 (MQ=255)                                                                                                         gAAAGCGGGTGATAATGGCGTTACAGGCGGTTATAGCCAGTTTTTTGGCCTGAAACATCAGATGTCGTTCGATAACGGCATGAACT‑GGAATAACGCCTTGCGTTACGACGTTCACAACCTTGACAGCAGCCGCTCGATTGCATTTGGCAac                                             <  1:174976/151‑1 (MQ=255)                                                                                                          aaaGCGGGTGATAATGGCGTTACAGGCGGTTTTAGCCCGGTTTTTTGCCTGGAACAAAAGAAGTTGTTTGATAAAGGCATGGAAT‑GGGAAAAAGCCCTTGGTTTAGAAGGTCACCACCCTTACAACAGCCGCCCGCTTTTAttttggaa                                              >  1:767120/1‑144 (MQ=255)                                                                                                             gCGGGTGATAATGGCGTTACAGGCGGTTTTAACCAGGTTTTTTGGCTGAAAAATCAAATGTTGTTCGATAAAGGCATGAAATGGGAAAAAACCCTTG‑GGTACGACGGTTACAAACTTTTAAACAGCCCCCCCGTTGCAttttggaaaa                                            >  1:832608/1‑141 (MQ=255)                                                                                                                            gTTACAGGCGGTTATAGCCAGTTTTTTGGCCTGAAACATCAGATGTCGTTCGATAACGGCATGAACT‑GGAATAACGCCTTGCGTTACGACGTTCACAACCTTGACAGCAGCCGCTCGATTGCATTTGGCAACACGAACAAAACGGCTGATa                          <  1:273561/151‑1 (MQ=255)                                                                                                                            gTTACAGGCGGTTATAGCCAGTTTTTTGGCCTGAAACATCAGATGTCGTTCGATAACGGCATGAACT‑GGAATAACGCCTTGCGTTACGACGTTCACAACCTTGACAGCAGCCGCTCGATTGCATTTGGCAACACGAACAAAACGGCTGATa                          <  2:314618/151‑1 (MQ=255)                                                                                                                                cAGGCGGTTATAGCCAGTTTTTTGGCCTGAAACATCAGATGTCGTTCGATAACGGCATGAACT‑GGAATAACGCCTTGCGTTACGACGTTCACAACCTTGACAGCAGCCGCTCGATTGCATTTGGCAACACGAACAAAACGGCTGATACCGa                      <  2:170338/151‑1 (MQ=255)                                                                                                                                  ggCGGTTATAGCCAGTTTTTTGGCCTGAAACATCAGATGTCGTTCGATAACGGCATGAACT‑GGAATAACGCCTTGCGTTACGACGTTCACAACCTTGACAGCAGCCGCTCGATTGCATTTGGCAACACGAACAAAACGGCTGATACCGACg                    <  2:637117/151‑1 (MQ=255)                                                                                                                                    cGGTTATAGCCAGTTTTTTGGCCTGAAACATCAGATGTCGTTCGATAACGGCATGAACT‑GGAATAACGCCTTGCGTTACGACGTTCACAACCTTGACAGCAGCCGCTCGATTGCATTTGGCAACACGAACAAAACGGCTGATACCGACGTg                  >  2:2967/1‑151 (MQ=255)                                                                                                                                     ggTTATAGCCAGTTTTTTGGCCTGAAACATCAGATGTCGTTCGATAACGGCATGAACT‑GGAATAACGCCTTGCGTTACGACGTTCACAACCTTGACAGCAGCCGCTCGATTGCATTTGGCAACACGAACAAAACGGCTGATACCGACGTg                  >  1:378302/1‑150 (MQ=255)                                                                                                                                       ttATAGCCAGTTTTTTGGCCTGAAACATCAGATGTCGTTCGATAACGGCATGAACT‑GGAATAACGCCTTGCGTTACGACGTTCACAACCTTGACAGCAGCCGCTCGATTGCATTTGGCAACACGAACAAAACGGCTGATACCGACGTGaa                >  2:481944/1‑150 (MQ=255)                                                                                                                                        tataGCCAGTTTTTTGGCCTGAAACATCAGATGTCGTTCGATAACGGCATGAACT‑GGAATAACGCCTTGCGTTACGACGTTCACAACCTTGACAGCAGCCGCTCGATTGCATTTGGCAACACGAACAAAACGGCTGATACCGACGTGaaa               <  2:840986/150‑1 (MQ=255)                                                                                                                                           aGCCAGTTTTTTGGCCTGAAACATCAGATGTCGTTCGATAACGGCATGAACT‑GGAATAACGCCTTGCGTTACGACGTTCACAACCTTGACAGCAGCCGCTCGATTGCATTTGGCAACACGAACAAAACGGCTGATACCGACGTGAAAcag            <  2:621870/150‑1 (MQ=255)                                                                                                                                                     ttGGCCTGAAACATCAGATGTCGTTCGATAACGGCATGAACT‑GGAATAACGCCTTGCGTTACGACGTTCACAACCTTGACAGCAGCCGCTCGATTGCATTTGGCAACACGAACAAAACGGCTGATACCGACGTGAAACAGCAGTACCTgg  >  2:356138/1‑150 (MQ=255)                                                                                                                                                      tGGCCTGAAACATCAGATGTCGTTCGATAACGGCATGAACT‑GGAATAACGCCTTGCGTTACGACGTTCACAACCTTGACAGCAGCCGCTCGATTGCATTTGGCAACACGAACAAAACGGCTGATACCGACGTGAAACAGCAGTACCTgg  >  2:763678/1‑149 (MQ=255)                                                                                                                                                       |                                                                                                                                                     ACCGAATACGACATGCTGGCATTGCGTAAAACTATCGACCTGAGCGAAAGCCAGACGATGAGTCTGGAGTACGGTATCGCTCGTCTCGATGGTGATGGTGCGCAGAAAGCGGGTGATAATGGCGTTACAGGCGGTTATAGCCAGTTTTTTGGCCTGAAACATCAGATGTCGTTCGATAACGGCATGAACT‑GGAATAACGCCTTGCGTTACGACGTTCACAACCTTGACAGCAGCCGCTCGATTGCATTTGGCAACACGAACAAAACGGCTGATACCGACGTGAAACAGCAGTACCTGG  >  NC_000913/1473252‑1473549

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑