Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	15,410	0	T	G	43.4%	91.0 / 11.7	53	intergenic (+112/‑35)	dnaJ/insL1	chaperone Hsp40, DnaK co‑chaperone/IS186 transposase
Reads supporting (aligned to +/- strand):  ref base T (2/28);  new base G (23/0);  total (25/28)
Fisher's exact test for biased strand distribution p-value = 4.81e-13
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GGTGTGAAGAAGTTTTTTGACGACCTGACCCGCTAACCTCCCCAAAAGCCTGCCCGTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGATCACTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCATATTGGTAAGCCCGAAGAACTGGATACTTCGGCACGTAATGCCGGGGCT  >  NC_000913/15263‑15534                                                                                                                                                    |                                                                                                                             ggTGTGAAGAAGTTTTTTGACGACCTGACCCGCTAACCTCCCCAAAAGCCTGCCCGTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGATCACTCCCATAAGCGCTAACTTAAGGGTtg                                                                                                                            <  2:526284/150‑1 (MQ=255)    gtgAAGAAGTTTTTTGACGACCTGACCCGCTAACCTCCCCAAAAGCCTGCCCGTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGGTCACTCCCCTAAGCGCTAACTTAAGGGGTGTgg                                                                                                                         >  2:768572/1‑150 (MQ=255)      gaagaaGTTTTTTGACGACCTGACCCGCTAACCTCCCCAAAAGCCTGCCCGTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGATCACTCCCATAAGCGCTAACTTAAGGGTTGTGGTa                                                                                                                       <  2:668707/150‑1 (MQ=255)       aagaagTTTTTTGACGACCTGACCCGCTAACCTCCCCAAAAGCCTGCCCGTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGGTCACTCCCCTAAGCGCCAACTTTAGGGGTGTGGTAtt                                                                                                                     >  1:864648/1‑151 (MQ=255)              tttttGACGACCTGACCCGCTAACCTCCCCAAAAGCCTGCCCGTGGGCAGGCCTGGGTAAAAATAGGGTGCGTCGAAGATATGCGAGCACCTGTAAAGTGGCGGGGATCACTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCt                                                                                                               <  2:16073/150‑1 (MQ=255)                 ttGACGACCTGACCCGCTAACCTCCCCAAAAGCCTGCCCGTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGATCACTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGat                                                                                                            <  1:344833/150‑1 (MQ=255)                  tGACGACCTGACCCGCTAACCTCCCCAAAAGCCTGCCCGTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGATCACTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGata                                                                                                           <  1:1008406/150‑1 (MQ=255)                  tGACGACCTGACCCGCTAACCTCCCCAAAAGCCTGCCCGTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGATCACTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGata                                                                                                           <  1:945422/150‑1 (MQ=255)                   gacgacCTGACCCGCTAACCTCCCCAAAAGCCTGCCCGTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGGTCACCCCCCTAAACGCTAACTTTAAGGGTGTGGGATTTAGCCTg                                                                                                              >  1:819787/1‑146 (MQ=255)                   gacgacCTGACCCGCTAACCTCCCCAAAAGCCTGCCCGTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGATCACTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATg                                                                                                         <  2:597193/151‑1 (MQ=255)                   gacgacCTGACCCGCTAACCTCCCCAAAAGCCTGCCCGTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGATCACTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATg                                                                                                         <  1:899891/151‑1 (MQ=255)                     cgacCTGACCCGCTAACCTCCCCAAAAGCCTGCCCGTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGAGCACTCCCCCAAGCGCCAAATTTAGGGGTGTGGGATTACGCCTGatat                                                                                                          >  2:135852/1‑148 (MQ=255)                      gacCTGACCCGCTAACCTCCCCAAAAGCCTGCCCGTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGGTCACTCCCATAAGCGCTAACTTAAGGGGTGTGGGATTACGCCTGATATGAtt                                                                                                      >  2:500856/1‑151 (MQ=255)                      gacCTGACCCGCTAACCTCCCCAAAAGCCTGCCCGTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGATCACTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGAtt                                                                                                      <  2:430526/151‑1 (MQ=255)                       acCTGACCCGCTAACCTCCCCAAAAGCCTGCCCGTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGGTCACTCCCATAAAGGCTAACATAAGGGGTGTGGGGTTTCGCCTGaaattgttt                                                                                                     >  1:492817/1‑146 (MQ=255)                        ccTGACCCGCTAACCTCCCCAAAAGCCTGCCCGTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGGGCACTCCCCTAAAAGCTAACTTAAAGGGTGTGGGGTTTCGCCTGATATGAttt                                                                                                     >  1:233966/1‑150 (MQ=255)                        ccTGACCCGCTAACCTCCCCAAAAGCCTGCCCGTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGATCACTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTa                                                                                                    <  2:953540/151‑1 (MQ=255)                         cTGACCCGCTAACCTCCCCAAAAGCCTGCCCGTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGGTGACTCCCCTAAACGCTAACTTAAGGGGTGTGGGATTACGCCCGGTATGAttt                                                                                                     >  2:603804/1‑149 (MQ=255)                           gACCCGCTAACCTCCCCAAAAGCCTGCCCGTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGATCACTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAAc                                                                                                  <  2:347621/150‑1 (MQ=255)                           gACCCGCTAACCTCCCCAAAAGCCTGCCCGTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGATCACTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAAc                                                                                                  <  2:213918/150‑1 (MQ=255)                            aCCCGCTAACCTCCCCAAAAGCCTGCCCGTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGATCACTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTaa                                                                                                   <  1:789135/148‑1 (MQ=255)                                 cTAACCTCCCCAAAAGCCTGCCCGTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGGTCACTCCCCTAAAAGCTAACTTAAGGGGTGGGGGATTACGCCCGGTATGAttttaagggcc                                                                                             >  2:316778/1‑141 (MQ=255)                                   aaCCTCCCCAAAAGCCTGCCCGTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGATCACTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATg                                                                                         <  2:624702/151‑1 (MQ=255)                                        ccccAAAAGCCTGCCCGTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGGGCACTCCCCTAAGCGCTAACTTTAGGGGTGTGGGATTTAGCCTGCTATGATTTAACGTGCCGATGaa                                                                                       >  1:1001372/1‑148 (MQ=37)                                           cAAAAGCCTGCCCGTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGATCACTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTActc                                                                                 <  2:134722/151‑1 (MQ=255)                                                gCCTGCCCGTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGATCACTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACg                                                                            <  1:918751/151‑1 (MQ=255)                                                     cccGTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGATCACTCCCCTAAGCGCTAACTTTAGGGGTGTGGGATTACGCCTGGTATGATTTAACGTGCCGATGAATTAATCTCACGATaa                                                                        >  2:57415/1‑150 (MQ=25)                                                       cGTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGGTCACTCCCATAAACGCTAACTTAAGGGGTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAAATACTCTCACGATaa                                                                        >  2:476075/1‑148 (MQ=255)                                                        gTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGATCACTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTgg                                                                    <  1:914206/151‑1 (MQ=255)                                                          gggCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCTGGGATCACTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTGGTc                                                                  <  1:552315/151‑1 (MQ=255)                                                            gCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGATCACTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTGGTCAg                                                                <  1:260726/151‑1 (MQ=255)                                                              aGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGGTGACTCCCCTAAACGCTAAATTAAGGGGTGGGGGATTAAGCCTGATATGATTTAAAGTGCCGGTGAATTACTCTCACGATAAATGGTCa                                                                 >  1:769160/1‑148 (MQ=255)                                                                gCCTGGGTAAAGATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGATCACTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTGGTCAGCAAt                                                            <  2:553432/151‑1 (MQ=255)                                                                gCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGATCACTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTGGTCAGCAAt                                                            <  1:572070/151‑1 (MQ=255)                                                                 ccTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGGTCACTCCCCTAAGCGCTAACTTAAAGGGTGTGGGATTAACCCCGATATGATTTTACGTGCCGATGAATTACTCTCACGATAAATTGTTAGCAAtt                                                           >  2:739584/1‑151 (MQ=21)                                                                 ccTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGGGCACTCCCCTAAACGCTAACTTAAGGGGTGTGGGATTACGCCTGATATGATTTAACATGCCGGTGAATTACTCTCACGATAAATGGTCAGCAAtt                                                           >  2:341154/1‑151 (MQ=21)                                                                 ccTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGATCACTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTGGTCAGCAAtt                                                           <  1:104467/151‑1 (MQ=255)                                                                   tGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGGTCACTCCCCTAAGCGCTAACTTTAGGGGTGTGGGTTTACGCCTGGTATGATTTAAAGGGCCGGTGAAATACTTTCACGAAAACTGGTTAGCAATTCt                                                         >  2:263116/1‑151 (MQ=255)                                                                    gggTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGAGCACTCCCATAAACGCCTACTTAAAGGGTGTGGGATTAAGCCCGATATGATTTTACGTGCCGAGGAATTATTCTCACGATAACTGGTCAGCAAtt                                                           >  1:114055/1‑148 (MQ=21)                                                                      gTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGAGCACTCCCATAAAAGCTAACTTAAAGGTTGTGGGATTACGCCTGATATGATTTAAAGTGCCGATGAATTAATCTCACGATAAATGGTCAGCAAATCttg                                                       >  2:698804/1‑148 (MQ=255)                                                                          aaaTAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGGTCACTCCCCAAAAAGGCAACTTAAGGGGTGTGGGGTTATGCCTGATATGATTTTAAGTGCCGATGAATTACTCTCACGAAAACTGGTCAGCAATTTTTGccc                                                    >  1:557179/1‑149 (MQ=18)                                                                          aaaTAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGATCACTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCat                                                  <  1:198834/151‑1 (MQ=255)                                                                             tAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGGTCACTCCCATAAGCGCTAAATTAAGGGGTGGGGGATTTCGCCTGATATGATTTAACGTGCCGATGAATTATTCTCACGATAAATTGTGAGCCAATTTGGCCCCTAtt                                               >  1:374517/1‑151 (MQ=18)                                                                                 gTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGGTCACTCCCCTAAACGCTAACTTTAGGGGTGTGGTATTACGCCTGATATTATTTAACGTGCCGATGAATTACTCTCACGAAAAATGGTCAGCAATTCTTGCCCCTAtt                                               >  2:337180/1‑147 (MQ=18)                                                                                 gTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGGTCACCCCCCTAAACGCCAACTTAAAGGGTGTGGGATTACGCCTGATATGATTTTAAGTGCCGATGAAATACTCTCACGATAAATGGTCAGCAAATCTTGCCCCTAtt                                               >  2:531434/1‑147 (MQ=255)                                                                                        gAAGATATGCGAGCACCTGTAAAGTGGCGGGGGTCACCCCCCTAAGCGCTAACTTAAGGGGTGTGGGATTACGCCTGATATGATTTAACGTGCCGCTGAATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCATATTTGTAAGccc                                      >  2:692048/1‑149 (MQ=17)                                                                                            atatGCGAGCACCTGTAAAGTGGCGGGGATCACTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCATATTGGTAAGCCCgaagaa                                <  2:919873/151‑1 (MQ=255)                                                                                              atGCGAGCACCTGTAAAGTGGCGGGGGTCACTCCCCTAAACGCTAAATTAAAGGGTGTGGGGTTACGCCTGATATGATTTAAAGTGCCGCTGAAATAATCTCACCATAAATGGGCAGCAATTCTGGGCCCTATTTGGAAACCCgaaaaa                                >  1:900699/1‑149 (MQ=255)                                                                                                      aCCTGTAAAGTGGCGGGGATCACTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCATATTGGTAAGCCCGAAGAACTGGATACtt                      <  1:603749/151‑1 (MQ=255)                                                                                                               gTGGCGGGGATCACTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCATATTGGTAAGCCCGAAGAACTGGATACTTCGGCACGTa             <  2:1001472/151‑1 (MQ=37)                                                                                                                         tCACTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCATATTGGTAAGCCCGAAGAACTGGATACTTCGGCACGTAATGCCGGGGc   >  2:1000811/1‑151 (MQ=32)                                                                                                                          cACTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCATATTGGTAAGCCCGAAGAACTGGATACTTCGGCACGTAATGCCGGGGct  <  1:18603/151‑1 (MQ=31)                                                                                                                          cACTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCATATTGGTAAGCCCGAAGAACTGGATACTTCGGCACGTAATGCCGGGGct  <  2:12664/151‑1 (MQ=31)                                                                                                                                                    |                                                                                                                             GGTGTGAAGAAGTTTTTTGACGACCTGACCCGCTAACCTCCCCAAAAGCCTGCCCGTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGATCACTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCATATTGGTAAGCCCGAAGAACTGGATACTTCGGCACGTAATGCCGGGGCT  >  NC_000913/15263‑15534

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑