Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	753,125	0	T	A	47.2%	59.5 / 29.7	53	intergenic (‑330/+60)	ybgD/gltA	putative fimbrial‑like adhesin protein/citrate synthase
Reads supporting (aligned to +/- strand):  ref base T (25/3);  new base A (0/25);  total (25/28)
Fisher's exact test for biased strand distribution p-value = 4.40e-12
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TCATTTTCATAGGGTTATAAATGCGACTACCATGAAGTTTTTAATTGAAAGTATTGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTTAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACAGCTGACGC‑GGACGGGCAATCTTCATACCGTCACTGTGCA  >  NC_000913/752975‑753273                                                                                                                                                       |                                                                                                                                                      tCATTTTCATAGGGTTATAAATGCGACTACCATGAAGTTTTTAATTGAAAGTATTGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTTAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCatat                                                                                                                                                       >  1:554323/1‑151 (MQ=255)        cATAGGGTTATAAATGCGACTACCATGAAGTTTTTAATTGAAAGTATTGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTTAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATc                                                                                                                                                >  2:630791/1‑151 (MQ=255)                    aaTGCGACTACCATGAAGTTTTTAATTGAAAGTATTGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTTAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCatat                                                                                                                                    >  2:288405/1‑151 (MQ=255)                      tGCGACTACCATGAAGTTTTTAATTGAAAGTATTGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTTAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATg                                                                                                                                   >  1:474705/1‑150 (MQ=255)                               cATGAATTTTTTAATTAAAATTATTGGGTTGCTGATAATTTGAGTTTTTCTATTTTTTTTAAATATTTATATAGGTCTGTTAATGGATTTTATTTTTACATTTTTTTGTGTTTAGGAATAAAAAAATCAACCCGCCATATGAACGGCGGGt                                                                                                                         <  1:285417/151‑1 (MQ=255)                               cATGAAGTTTTTAATTGAAAGTATTGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTTAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCggg                                                                                                                          >  2:318270/1‑150 (MQ=255)                                aTGAATTTTTAAATAAAAAGTATTGGTTTATTGATATTTAAAATTTTTCTATTCTTTTAAAATTTATATATAGGTGTTTGAATGGTTTTTTTTTTAACAATTTTTTGTGTTTCGGCAAAAAAAAATCACCCCGCCATATGAACGGCGGGt                                                                                                                         <  2:14757/150‑1 (MQ=255)                                      tttttAATTGAAAGTATTGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTTAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTaaaa                                                                                                                    >  2:402110/1‑149 (MQ=255)                                      tttttAATTGAAAGTATGGGTTTGTTGATATTTTGAGTTTTTTTTTTTTTTTTAAATATTTATATAGGTCTGTTAAGGGTTTTTATTTTTACAATTTTTTGTTTTTAGGCATAAAAAAACCACCCCGCCATATGAAcggcgg                                                                                                                           <  1:334696/142‑1 (MQ=255)                                        tttAATAAAAAGTTTTGGTTGTCTGATATTTTTGGTTTTTATTTTCTTTTAAAATTTTTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTTTTTTTGGCAATAAAAAAATCACCCCGCCATATGAACGGCGGGTTa                                                                                                                       <  2:391265/144‑1 (MQ=255)                                          tAATTGAAAGTATTGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTTAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATAttt                                                                                                               >  2:473387/1‑150 (MQ=255)                                              tGAAAGTATTGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTTAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACaa                                                                                                           >  1:26094/1‑150 (MQ=255)                                                aaaGTATTGGTTTGCTGATAATTTGAGCTTTTTTTTTTTTTTTAAATATCTATATAGGTCTTTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATAAAAAAATCACCCCGCCATATGAACGGCGGGTTAAAATATTTACa                                                                                                            <  2:88336/147‑1 (MQ=255)                                                aaaGTATTGGGTTGCTGATAATTTGAGCTTTTCTATTCTTTTTAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTTTTTAGGCATAAAAAAACCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACtt                                                                                                        <  2:83380/151‑1 (MQ=255)                                                        gggTTGCTGATATTTTGAGCTTTTTTTTTCTTTTTAAATATCTATATAGGTTTGTTAATGGATTTTTTTTTTACAATTTTTTGTTTTTAGGAATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATc                                                                                                 <  2:658197/150‑1 (MQ=255)                                                         ggTTGCTGATAATTTGAGCTGTTCTATTCTTTTTAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAAtta                                                                                                >  1:34488/1‑148 (MQ=255)                                                            tGCTGATAATTTGAGCTGTTCTATTCTTTTTAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAAcc                                                                                             >  2:144332/1‑150 (MQ=255)                                                               tGATAATTTGAGCTGTTTTTTTTTTTTTAAATATTTAAATAGGTTTTTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATAAAAAAACCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCAt                                                                                           <  2:108203/149‑1 (MQ=255)                                                                   attttGATCTTTTCTTTTTTTTTAAAATATCTATATTGGTTTGTTAATAGATTTTATTTTTACATTTTTTTGTTTTTATAAATAAAAAAAACACCCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCAtt                                                                                          <  1:578532/144‑1 (MQ=255)                                                                      tggAGCTGTTTTTTTTTTTTAAAATATCTATATAGGTCTGTTAATGTTTTTTATTTTTATATTTTTTTGTTTTAAGCAATATAAAACTCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCtt                                                                                   <  2:466682/148‑1 (MQ=255)                                                                            tGTTCTATTCTTTTTAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATc                                                                             >  2:342357/1‑150 (MQ=255)                                                                             gTTCTATTCTTTTTAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGc                                                                           >  2:125900/1‑151 (MQ=255)                                                                                cTATTCTTTTTAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTTCAACTTAGCAATCAACCATTAAAGCTTGATATCGCttt                                                                        >  2:427525/1‑151 (MQ=255)                                                                                   ttttttttAAATATCTATATAGGTCTGTTAATGGTTTTTTTTTTTACAATTTTTTGTTTTTAGGAATAAAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTa                                                                      <  2:606961/147‑1 (MQ=255)                                                                                      tttttAAATTTTAATATAGTTTTATTAATGATTTTTATTTTTACATTTTTTTTTTTTTAGGAAAAAAAAAAACAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTaaa                                                                    <  1:376966/149‑1 (MQ=255)                                                                                      ttttaAAATATATATATGGTTTTGTAAATGCATTTATTTTTAACAATTTTTTTTTTTAAGAAAAAAAAAAATCACACCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTaaa                                                                    <  1:661778/149‑1 (MQ=255)                                                                                       ttttAAATATTTATAAAGGTTTGTTAATGGATTTTATTTTTAAAATTTTTTGTGTTTAGGAATAAAAAAACCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGt                                                                  <  2:459704/150‑1 (MQ=255)                                                                                        ttaaaaTATCTATATAGTTCTGTTAATGGTTTTTTTTTTTACATTTTTTTGTTTTTAGGCATAAAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTc                                                                 <  2:292840/147‑1 (MQ=255)                                                                                           aaaTATTTATATAGTTCTGTTAATGTTTTTTATTTTTAAATTTTTTTGTGTTTAGGAATAAAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTcgc                                                               <  1:31896/149‑1 (MQ=255)                                                                                           aaaTATTTATATAGGTCTTTTAATGTTTTTTATTTTTACAATTTTTTGTTTTTAGGAATAAAAAAATCACCCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTc                                                                 <  1:318246/147‑1 (MQ=255)                                                                                           aaaTATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTTAAGTcgcg                                                              >  2:204319/1‑150 (MQ=255)                                                                                                   atataGGTTTGTTAATGGTTTTTATTTTTAAAATTTTTTGTTTTTAGGAATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGttttt                                                         <  2:59243/147‑1 (MQ=255)                                                                                                    tttaGGTCTTTTAAGGGATTTTATTTTTAAATTTTTTTGTTTTTAGGCATAAAAAAACCATCCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTc                                                        <  2:31190/145‑1 (MQ=255)                                                                                                    tataGTTTTTTTAATGGTTTTTATTTTTACATTTTTTTGTTTATAGGCATAAAAAATCCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGGTTTTCata                                                     <  1:545551/150‑1 (MQ=255)                                                                                                     ataGTTCTTTAAATGTTTTTTATTTTAACAATTTTTTGTTTTTAGGCATAAAAAAACCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGtttt                                                          <  2:112998/144‑1 (MQ=255)                                                                                                      taGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGTTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGGCGCGTTTTTCATATc                                                   >  2:18457/1‑150 (MQ=255)                                                                                                       aGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCata                                                     >  1:626096/1‑147 (MQ=255)                                                                                                          tCTGTTAATGTATTTTATTTTTAAAATTTTTTGTGTTTAGGCATAAAAAAAACAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGt                                               <  1:204298/150‑1 (MQ=255)                                                                                                            tGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAAATTAGCAATCAACCATTAACGCTTGATATCGCTTTTTAAGTCGCGTTTTTCATATCCTGtat                                             >  1:491077/1‑150 (MQ=255)                                                                                                              ttAATGGTTTTTATTTTTACATTTTTTTGTGTTTAGACATAAAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGtata                                            <  2:542067/149‑1 (MQ=255)                                                                                                              ttAATGGTTTTTATTTTAACAATTTTTTGTGTTTAGGAATAAAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGtat                                             <  1:82554/148‑1 (MQ=255)                                                                                                                aaTGGATTTTATTTTTACAATTTTTTGTGTTTAGGAATAAAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACAg                                         <  1:386026/150‑1 (MQ=255)                                                                                                                  tGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTTAAGTCGCGTTTTTCATATCCTGTATACAGCt                                       >  2:382885/1‑150 (MQ=255)                                                                                                                    tatttttttttTAAATTTTTTTGTTTTTAGGATTAAAAAAACCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACAGCTGa                                     <  1:569394/149‑1 (MQ=255)                                                                                                                            tttaaaatttttttttttttAGAAATAAAAAAATCACCCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACAGCTGACGC‑GGACg                            <  1:493255/142‑1 (MQ=255)                                                                                                                                 cAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACAGCTGACGC‑GGACGGGCaa                       >  2:325902/1‑150 (MQ=255)                                                                                                                                    ttttttGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAAACATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACAGCTGACGC‑GGACGGGCAAACtt                   >  2:255564/1‑151 (MQ=255)                                                                                                                                       tttGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAATCGCGTTTTTCATATCCTGTATACAGCTGACGC‑GGACGGGCAATCTTCa                 >  2:119047/1‑150 (MQ=255)                                                                                                                                       tttGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGGTAAAATAATTACAACTTAGCAATCAACCATTAACGCTTGGTATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACAGCTGAAGC‑GGACGGGCAATATTCAt                >  1:658776/1‑151 (MQ=255)                                                                                                                                         tgtgTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTTAAGTCGCGgtttt                                                         >  2:390367/1‑109 (MQ=255)                                                                                                                                         tgtgTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACAGCTGACGC‑GGACGGGCAATCTTCATa               >  2:658255/1‑150 (MQ=255)                                                                                                                                           tttttAGGCATAAAAAAACCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACAGCTGACGC‑GGACGGGCAATCTTCATa               <  2:647061/146‑1 (MQ=255)                                                                                                                                               tAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACAGCTGACGC‑GGACGGGCAATCTTCATACCGTCAc        >  2:605370/1‑151 (MQ=255)                                                                                                                                                aGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACAGCTGACGC‑GGACGGGCAATCTTCATACCGTCAc        >  1:248679/1‑150 (MQ=255)                                                                                                                                                 ggaataaAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACAGCTGACGC‑GGACGGGCAATCTTCATACCGTCACtg      <  2:298934/148‑1 (MQ=255)                                                                                                                                                    atatAAAAATCAACCCGCCATATGAACGGCGGGGTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTGCGGTTTTTCTAATCCTGTATAAAGCTG‑CGCGGGGCGGGCAAttttacaaccgcccc        >  2:529362/1‑135 (MQ=255)                                                                                                                                                      ataAAAATAACCCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACAGCTGACGC‑GGACGGGCAATCTTCATACCGTCACTGTGCa  <  2:213575/150‑1 (MQ=255)                                                                                                                                                       |                                                                                                                                                      TCATTTTCATAGGGTTATAAATGCGACTACCATGAAGTTTTTAATTGAAAGTATTGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTTAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACAGCTGACGC‑GGACGGGCAATCTTCATACCGTCACTGTGCA  >  NC_000913/752975‑753273

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑