Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,601,160	0	G	A	43.9%	42.2 / 20.4	42	F309F (TTC→TTT)	ftsX	putative ABC transporter permease
Reads supporting (aligned to +/- strand):  ref base G (18/5);  new base A (0/18);  total (18/24)
Fisher's exact test for biased strand distribution p-value = 1.69e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CACGCTTTTATTATTCAGGCGTAAAGTGGCGTAAATGTTGTACCGTGGCAAGCCACGCTGCCACCCAGCCAATCATCGAGCATACCAGCAGCAATAGCAGGCATTCATCGAATGATAAGCCATTGATATCAAACTTCGTTCCGAAAA‑CC‑TGTGCCACTTCCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACAGGAACGGGCGCAGGATGAATCCATCTGTCGCA  >  NC_000913/3601018‑3601301                                                                                                                                               |                                                                                                                                                cacGCTTTTATTATTCAGGCGTAAAGTGGCGTAAATGTTGTACCGTGGCAAGCCACGCTGCCACCCAGCCAATCATCGAGCATACCAGCAGCAATAGCAGGCATTCATCGAATGATAAGCCATTGATATCAAACTTCGTTCCGAAAA‑CC‑tg                                                                                                                                       <  2:483216/151‑1 (MQ=255)   cGCTTTTATTATTCAGGCGTAAAGTGGCGTAAATGTTGTACCGTGGCAAGCCACGCTGCCACCCAGCCAATCATCGAGCATACCAGCAGCAATAGCAGGCATTCATCGAATGATAAGCCATTGATATCAAACTTCGTTCCGAAAA‑CC‑tgtg                                                                                                                                     >  2:120895/1‑151 (MQ=255)     cTTTTATTATTCAGGCGTAAAGTGGCGTAAATGTTGTACCGTGGCAAGCCACGCTGCCACCCAGCCAATCATCGAGCATACCAGCAGCAATAGCAGGCATTCATCGAATGATAAGCCATTGATATCAAACTTCGTTCCGAAAA‑CC‑TGTGcc                                                                                                                                   >  1:431009/1‑151 (MQ=255)       tttATTATTCAGGCGTAAAGTGGCGTAAATGTTGTACCGTGGCAAGCCACGCTGCCACCCAGCCAATCATCGAGCATACCAGCAGCAATAGCAGGCATTCATCGAATGATAAGCCATTGATATCAAACTTCGTTCCGAAAA‑CC‑TGTGCCa                                                                                                                                  <  2:536589/150‑1 (MQ=255)            tattCAGGCGTAAAGTGGCGTAAATGTTGTACCGTGGCAAGCCACGCTGCCACCCAGCCAATCATCGAGCATACCAGCAGCAATAGCAGGCATTCATCGAATGATAAGCCATTGATATCAAACTTCGTTCCGAAAA‑CC‑TGTGCCACTTcc                                                                                                                             <  1:78698/150‑1 (MQ=255)               tCAGGCGTAAAGTGGCGTAAATGTTGTACCGTGGCAAGCCACGCTGCCACCCAGCCAATCATCGAGCATACCAGCAGCAATAGCAGGCATTCATCGAATGATAAGCCATTGATATCAAACTTCGTTCCGAAAA‑CC‑TGTGCCACTTCCGCa                                                                                                                          <  2:404761/150‑1 (MQ=255)                cAGGCGTAAAGTGGCGTAAATGTTGTACCGTGGCAAGCCACGCTGCCACCCAGCCAATCATCGAGCATACCAGCAGCAATAGCAGGCATTCATCGAATGATAAGCCATTGATATCAAACTTCGTTCCGAAAA‑CC‑TGTGCCACTTCCGCAAc                                                                                                                        >  1:261521/1‑151 (MQ=255)                cAGGCGTAAAGTGGCGTAAATGTTGTACCGTGGCAAGCCACGCTGCCACCCAGCCAATCATCGAGCATACCAGCAGCAATAGCAGGCATTCATCGAATGATAAGCCATTGATATCAAACTTCGTTCCGAAAA‑CC‑TGTGCCACTTCCGCAAc                                                                                                                        >  2:520888/1‑151 (MQ=255)                   gggTAAAGTGGCGTAAATGTTCTACCGTGGCTAGCCACGCTGCCACCCAGCCAATCATCACGCATACCAGCAGCAATAGCAGGCATTCATCGAATGATAAGCCATTGATATCAAACTTCGTTCCGAAAA‑CC‑TGTGCCACTTCCTCAAccgc                                                                                                                     >  1:149395/3‑151 (MQ=255)                   gCGTAAAGTGGCGTAAATGTTGTACCGTGGCAAGCCACGCTGCCACCCAGCCAATCATCGAGCATACCAGCAGCAATAGCAGGCATTCATCGAATGATAAGCCATTGATATCAAACTTCGTTCCGAAAA‑CC‑TGTGCCACTTCCGCAAccgc                                                                                                                     >  2:30242/1‑151 (MQ=255)                       aaaGTGGCGTAAATGTTGTACCGTGGCAAGCCACGCTGCCACCCAGCCAATCATCGAGCATACCAGCAGCAATAGCAGGCATTCATCGAATGATAAGCCATTGATATCAAACTTCGTTCCGAAAA‑CC‑TGTGCCACTTCCGCAACCGCCGAt                                                                                                                 >  1:585567/1‑151 (MQ=255)                        aaGTGGCGTAAATGTTGTACCGTGGCAAGCCACGCTGCCACCCAGCCAATCATCGAGCATACCAGCAGCAATAGCAGGCATTCATCGAATGATAAGCCATTGATATCAAACTTCGTTCCGAAAA‑CC‑TGTGCCACTTCCGCAACCGCCGATg                                                                                                                >  2:590056/1‑151 (MQ=255)                                        gtACCGTGGCAAGCCACGCTGCCACCCAGCCAATCATCGAGCATACCAGCAGCAATAGCAGGCATTCATCGAATGATAAGCCATTGATATCAAACTTCGTTCCGAAAA‑CC‑TGTGCCACTTCCGCAACCGCCGATGACAATCGCAGCAcc                                                                                                  >  1:259830/1‑149 (MQ=255)                                          cccgggacAACCCCCGCTCCCCCCCACCAAACCACCGACCATCCCAGCACAAATGGCAGGCATTCACCAAATAATACGCATTAAATATAAACCTTCGTCCCAAAAC‑CC‑TGTCCCCCTCCCGCAACCGCCGATGACAATCGCAGCACCa                                                                                                 <  1:128118/141‑1 (MQ=255)                                           ccGTGGCAAGCCACGCTGCCACCCAGCCAATCATCGAGCATACCAGCAGCAATAGCAGGCATTCATCGAATGATAAGCCATTGATATCAAACTTCGTTCCGAAAA‑CC‑TGTGCCACTTCCGCAACCGCCGATGACAATCGCAGCACCAGAAt                                                                                             >  1:420655/1‑151 (MQ=255)                                           ccGTGGCAACCCCCCCTCCCACCCACCAAATCACCAACCATCCCAGCAGAAATAGCGGGCTTCAATAAAATGATAACCCTTTGATATAAACCTTCGTTCCAAAAC‑CC‑TGCGCCCCTCCCGCAACCGCCGATGACAATCGCAGCACCa                                                                                                 <  1:453198/147‑1 (MQ=255)                                                      cccgcccccccccAGCAAATCATCGAGCATACCAGAAGAAATAGCAGGCTTTCATCAAATAATAAGCCATTAATATCAACCTTCGTCCCGAAAC‑CC‑TGTCCCCCTCCCGAAACCGCCGATGACAATCGCAGCACCAGAATTTCt                                                                                         <  2:125750/134‑1 (MQ=255)                                                      cccGCTCCCACCCAGCCAATCACCGACCATACCAGCAAAAAAACCAGGCTTACAGAAAATGATAAGCTATTTATATCAACCCTCG‑TCCAAAAA‑CCTTGCCCCCCTCCCGCACCCGCCGATGACAATCGCAGCACCAGAATTTCTGACaaa                                                                                   <  2:439598/148‑1 (MQ=255)                                                        cGCTGCCCCCCAGCAAACCACCGACCACCCCAGCAAAAATAGCTGGCATTCATCAAATAATAAGCCTTTAATAACACGCTTCGCCCCAAAAC‑CC‑TTCCCCCCTCCCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAAtt                                                                                <  1:437414/151‑1 (MQ=255)                                                             ccccccAGCCAATCACCGAGCATCCCAGAAGAAATAGCGGGCATTCATCAAATGATAAGCCTTTGATATCAACCTTCGTCCCAAAAC‑CC‑TGTCCCCCTCCCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAAt                                                                             <  2:50306/146‑1 (MQ=255)                                                             ccccccAACCAATCCTCGAGCACACCAACAGAAATAGCAGGCTTTAAAGGAATAATAAGCCATTTATACCAAACTTCGTCCCAAAAC‑CC‑TGTGCCCCTCCCCCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGa                                                                           <  2:215120/148‑1 (MQ=255)                                                                   acccAACCATCGATCATACCAGCAAAAATAGCAGGCATTAACCAAATGATAAGCCATTGATATAAACCTTCGTCCCAAAAC‑CC‑TGTCCCCCTCCCGAAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGacaaca                                                                      <  2:459743/148‑1 (MQ=255)                                                                       aaTCATCGAGCATACCAGAAAAAATAGCAGACATACATCAAATGATAACCCATTGATATCAAACTTCGTCCCAAAAC‑CC‑TGTGCCACTTCCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATgcg                                                                 <  2:178672/151‑1 (MQ=255)                                                                       aaTCACCGACCACCCCAGCAGAAAAAGCAGGCATTCATAAAATAAAAAGCCATTGATAACAACCTTCGTCCCAAAAC‑CC‑TGTCCCACTCCCAAAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATgcg                                                                 <  1:116717/151‑1 (MQ=255)                                                                           atcGAGCATACCAGCAGCAATAGCAGGCATTCATCGAATGATAAGCCATTGATATCAAACTTCGTTCCGAAAA‑CC‑TGTGCCACTTCCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGcc                                                               >  2:326813/1‑149 (MQ=255)                                                                           atcGAGCATACCAGCAGAAATAGCAGGCTTTCATCAAATGATAACCCTTTAATATCAAACTTCTTTCCAAAAC‑CC‑TGTGCCCCTTCCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAg                                                             <  2:46753/151‑1 (MQ=255)                                                                                  aTACCAGCAAAAATAGCAGACATTCAACGAATGAAAAGCTATTAATATAAACCTTCTTCCCAAAAC‑CC‑TGCGCCTCTCCCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGaaaa                                                         <  2:261219/148‑1 (MQ=255)                                                                                    aCCAGAAGAAATAGCAGGCATTCAGCGAATGATAAGCCATTGATAAAAACCTTCTTCCCAAAAC‑CC‑TGTGCCCCTTCCGAAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAAt                                                        <  2:574377/147‑1 (MQ=255)                                                                                      cagcagCAATAGCAGGCATTCATCGAATGATAAGCCATTGATATCAAACTTCGTTCCGAAAA‑CC‑TGTGCCACTTCCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCcagc                                                  >  2:211001/1‑151 (MQ=255)                                                                                             aaaagcagcCATTCATCGAATAAAAACCCATTAATAACAACCTTCTTCCCAAAAC‑CC‑TGTCCCACTCCCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTgcg                                            <  2:369150/147‑1 (MQ=255)                                                                                             aaTAGCAGGCATTCATCGAATGATAAGCCATTGATATCAAACTTCGTTCCGAAAA‑CC‑TGTGCCACTTCCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTgcgc                                           >  2:621908/1‑151 (MQ=255)                                                                                                        ttCATCGAATGATAAGCCATTGATATCAAACTTCGTTCCGAAAA‑CC‑TGTGCCACTTCCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACAgg                                >  2:339881/1‑151 (MQ=255)                                                                                                           atcaaataaaaccccATTAATATAAACCTTCTTCCCAAAAC‑CC‑TGTCCCATTCCCACAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACAGGaa                              <  1:155197/137‑1 (MQ=255)                                                                                                           aTCAAATAATAACCTATTAATATCAACCTTCTTCCCAAAAC‑CC‑TGTCCCACTCCCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACAGGAAc                             <  2:515119/151‑1 (MQ=255)                                                                                                               aataaaaggCCTTTAATATAAACCTCCGTCCCAAAAC‑CC‑TGTCCCACTCCCACAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACAGGAACgg                           <  1:585263/141‑1 (MQ=255)                                                                                                               aaTGATAAGCCATTGATATCAAACTTCGTTCCGAAAA‑CC‑TGTGCCACTTCCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACAGGAACGGgc                         >  2:402049/1‑151 (MQ=255)                                                                                                                    tAAGCCATTGATATCAAACTTCGTTCCGAAAA‑CC‑TGTGCCACTTCCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACAGGAACGGGCGCAgg                    >  2:243084/1‑151 (MQ=255)                                                                                                                      aGCCATTGATATCAAACTTCGTTCCGAAAA‑CC‑TGTGCCACTTCCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACAGGAACGGGCGCAGGAt                  >  2:156143/1‑151 (MQ=255)                                                                                                                                  cAAACTTCGTTCCGAAAA‑CC‑TGTGCCACTTCCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACAGGAACGGGCGCAGGATGAATCCATCTGt      >  1:468372/1‑151 (MQ=255)                                                                                                                                   aaccTTCGTTCCAAAAC‑CC‑TGTGCCCCTCCCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACAGGAACGGGCGCAGGATGAATCCATCt        <  2:452445/145‑1 (MQ=255)                                                                                                                                    aaCCTCCTTCCCAAAACCC‑TGCGCCCCTCCCGAAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACAGGAACGGGCGCAGGATGAATCCATCt        <  2:100838/148‑1 (MQ=255)                                                                                                                                        tCGTCCCAAAAC‑CC‑TGTCCCCCCCCCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACAGGAACGGGCGCAGGATGAATCCATCTGTCGCa  <  1:366145/149‑1 (MQ=255)                                                                                                                                               |                                                                                                                                                CACGCTTTTATTATTCAGGCGTAAAGTGGCGTAAATGTTGTACCGTGGCAAGCCACGCTGCCACCCAGCCAATCATCGAGCATACCAGCAGCAATAGCAGGCATTCATCGAATGATAAGCCATTGATATCAAACTTCGTTCCGAAAA‑CC‑TGTGCCACTTCCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACAGGAACGGGCGCAGGATGAATCCATCTGTCGCA  >  NC_000913/3601018‑3601301

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑