Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,601,176	0	T	C	42.9%	47.3 / 21.2	43	E304G (GAA→GGA)	ftsX	putative ABC transporter permease
Reads supporting (aligned to +/- strand):  ref base T (19/5);  new base C (0/18);  total (19/24)
Fisher's exact test for biased strand distribution p-value = 1.06e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TATTCAGGCGTAAAGTGGCGTAAATGTTGTACCGTGGCAAGCCACGCTGCCACCCAGCCAATCATCGAGCATACCAGCAGCAATAGCAGGCATTCATCGAATGATAAGCCATTGATATCAAACTTCGTTCCGAAAA‑CC‑TGTGCCACTTCCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACAGGAACGGGCGCAGGATGAATCCATCTGTCGCACCAATCAGTTTCTGTACG  >  NC_000913/3601029‑3601319                                                                                                                                                      |                                                                                                                                                tattCAGGCGTAAAGTGGCGTAAATGTTGTACCGTGGCAAGCCACGCTGCCACCCAGCCAATCATCGAGCATACCAGCAGCAATAGCAGGCATTCATCGAATGATAAGCCATTGATATCAAACTTCGTTCCGAAAA‑CC‑TGTGCCACTTcc                                                                                                                                               <  1:78698/150‑1 (MQ=255)    tCAGGCGTAAAGTGGCGTAAATGTTGTACCGTGGCAAGCCACGCTGCCACCCAGCCAATCATCGAGCATACCAGCAGCAATAGCAGGCATTCATCGAATGATAAGCCATTGATATCAAACTTCGTTCCGAAAA‑CC‑TGTGCCACTTCCGCa                                                                                                                                            <  2:404761/150‑1 (MQ=255)     cAGGCGTAAAGTGGCGTAAATGTTGTACCGTGGCAAGCCACGCTGCCACCCAGCCAATCATCGAGCATACCAGCAGCAATAGCAGGCATTCATCGAATGATAAGCCATTGATATCAAACTTCGTTCCGAAAA‑CC‑TGTGCCACTTCCGCAAc                                                                                                                                          >  2:520888/1‑151 (MQ=255)     cAGGCGTAAAGTGGCGTAAATGTTGTACCGTGGCAAGCCACGCTGCCACCCAGCCAATCATCGAGCATACCAGCAGCAATAGCAGGCATTCATCGAATGATAAGCCATTGATATCAAACTTCGTTCCGAAAA‑CC‑TGTGCCACTTCCGCAAc                                                                                                                                          >  1:261521/1‑151 (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)                                                                                                                                        a‑CC‑TGTGCCACTTCCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACAGGAACGGGCGCAGGATGAATCCATCTGTCGCACCAATCAGTTTCt       >  1:290489/1‑151 (MQ=255)                                                                                                                                           ccggttccACTACCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACAGGAACGGGCGCAGGATGAATCCATCTGTCGCACCAATCAGTTTCt       <  2:431068/144‑1 (MQ=255)                                                                                                                                             tgtgCCACTTCCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACAGGAACGGGCGCAGGATGAATCCATCTGTCGCACCAATCAGTTTCTGt     >  1:60988/1‑150 (MQ=255)                                                                                                                                               tgCCCCTCCCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTTATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACAGGAACGGGCGCAGGATGAATCCATCTGTCGCACCAATCAGTTTCTGt     <  1:120884/148‑1 (MQ=255)                                                                                                                                               tgCCACTTCCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACAGGAACGGGCGCAGGATGAATCCATCTGTCGCACCAATCAGTTTCTGTACg  >  2:630662/1‑151 (MQ=255)                                                                                                                                                      |                                                                                                                                                TATTCAGGCGTAAAGTGGCGTAAATGTTGTACCGTGGCAAGCCACGCTGCCACCCAGCCAATCATCGAGCATACCAGCAGCAATAGCAGGCATTCATCGAATGATAAGCCATTGATATCAAACTTCGTTCCGAAAA‑CC‑TGTGCCACTTCCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACAGGAACGGGCGCAGGATGAATCCATCTGTCGCACCAATCAGTTTCTGTACG  >  NC_000913/3601029‑3601319

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑