Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,435,718	0	G	A	44.2%	74.5 / 24.4	53	intergenic (‑99/+42)	uspF/ompN	stress‑induced protein, ATP‑binding protein/outer membrane pore protein N, non‑specific
Reads supporting (aligned to +/- strand):  ref base G (25/4);  new base A (0/23);  total (25/28)
Fisher's exact test for biased strand distribution p-value = 5.06e-11
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AGTTAATTCTGAATCGGAAATATCGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTT‑AGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTATAG  >  NC_000913/1435569‑1435859                                                                                                                                                       |                                                                                                                                              aGTTAATTCTGAATCGGAAATATCGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTT‑AGATCAAAGGAGgaag                                                                                                                                               <  1:348648/150‑1 (MQ=255)              tCGGAAATATCGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTT‑AGATCAAAGGAGGAAGAATAAGCAGaaaa                                                                                                                                  >  2:102845/1‑150 (MQ=255)                 gAAATATCGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTT‑AGATCAAAGGAGGAAGAATAAGCAGAAAAAGcc                                                                                                                              >  1:596077/1‑151 (MQ=255)                  aaaTATCGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTT‑AGATCAAAGGAGGAAGAATAAGCAGAAAAAGccc                                                                                                                             <  1:140150/151‑1 (MQ=255)                       tCGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTT‑AGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCa                                                                                                                         <  1:370190/150‑1 (MQ=255)                        cGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTT‑AGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCAt                                                                                                                        >  1:748499/1‑150 (MQ=255)                            aGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTT‑AGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAAc                                                                                                                     >  1:743805/1‑149 (MQ=255)                                aCAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTT‑AGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCggg                                                                                                               >  1:725327/1‑151 (MQ=255)                                          ttttGTTAATAAACCCTCTTGTTTTAGTATCCACAAAAAGTGTAACGCCAGATAACATTTTTTGTAAAAGGGCGGACTCCACTTTTTTATTTT‑AGACCAAAGAAGAAAAAAAAAGCAAAAAAACCCCGCCATAACAGCGGGCAggagga                                                                                                       <  1:244049/146‑1 (MQ=255)                                               ttaaaaaacCCTCCTTTTTTAGTATCCAAAAAAAGTGAACCGCAAGATGACTTTTTTTGTGAAATGAGGGAGTTCACATTTTTAATTT‑AGATAAAAGGAGAAAAAAAAAGCAAAAAAAGCCCGCCATAACAGCGGGCAGGAGGAttt                                                                                                    <  2:912773/142‑1 (MQ=255)                                               ttaaaaaacCCTCCTTTTTTAGTACCCGAAAAAAGTGAAACGCAAGATGCCTTTTTTTGTTTAAGGAGGGATTTCACTTTTTTATTTA‑AGAAAAAAGAAGAAAAAAAAAGAAAAAAAAGCCCGCCATAACAGCGGGCAGGAGGAttt                                                                                                    <  1:771857/142‑1 (MQ=255)                                                 cATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTT‑AGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACt                                                                                              >  1:360861/1‑151 (MQ=255)                                                 cATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTT‑AGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACt                                                                                              >  2:487313/1‑151 (MQ=255)                                                      aaCCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTT‑AGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATa                                                                                          >  1:170616/1‑150 (MQ=255)                                                             tGTTTTAGTACCCGAATAAAGTGAAACGCAAAATGACTTTTTTTGTGAAAGGACGGAGTTCACTTTTTAAATTA‑AAAAAAAAGGGGAAAGAATAAGAAAAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAg                                                                                    <  1:875014/149‑1 (MQ=255)                                                              gTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTT‑AGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGAcc                                                                                 >  2:499107/1‑151 (MQ=255)                                                               ttttAGTCTCCGAATAAAGTGTAACGCCAGATAACTTTTTTTGTGTAATGACGGAGTTCCTATTTTAAATTT‑AGATAAAAGGAGGAAAAATAAGCAAAAAAGGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAAcc                                                                                      <  2:398020/145‑1 (MQ=255)                                                               ttttAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTT‑AGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCt                                                                                >  1:622220/1‑151 (MQ=255)                                                                   aGTACCCGAAAAAAGTGAACCCCAAGATGACATTTTTGGTGAAAGGAGGGATTTCACTTTTTTAATTA‑AGATAAAAGGAGAAAAAAAAAAAAAAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTaa                                                                              <  1:688502/149‑1 (MQ=255)                                                                      aTCCGAAAAAAGTGTAACGCAAGATGACATTTTTGTTGAAAGGACGAAGTTCACATTTTTAATTT‑AGAAAAAAGGAGAAAAAAAAAGAAAAAAAACCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGc                                                                           <  1:884079/149‑1 (MQ=255)                                                                            aTAAAGTGTAACGCCAGATGACTCTTTTTGTGTAATGAGGGAGTTCATTTTTTTAATTA‑AGAAAAAAGGAGAAAAAAAAAGAAAAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAat                                                                     <  1:687645/149‑1 (MQ=255)                                                                             tAAAGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTT‑AGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATatc                                                                  >  2:683340/1‑151 (MQ=255)                                                                                aGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTT‑AGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATatcatc                                                               >  1:46528/1‑151 (MQ=255)                                                                                aGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTT‑AGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATatcatc                                                               >  2:13614/1‑151 (MQ=255)                                                                                     aaCGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTT‑AGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGt                                                            >  1:66943/1‑149 (MQ=255)                                                                                     aaCGCAAGATGACTTTTTTTGTGTAAGGAGGGAGTTCATTTTTTTATTTA‑AAAAAAAGGGAGAAAAAAAAAAAAAAAAAACCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTa                                                           <  1:158507/150‑1 (MQ=255)                                                                                     aaCCCCAGATGACTTTTTTTGTGTAAGGACGGATTTCACTTTTTTAATTT‑AGATAAAAGGAGAAAAAAAAAGCAAAAAAACCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGt                                                            <  2:163160/149‑1 (MQ=255)                                                                                        gCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTT‑AGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTag                                                          >  2:884536/1‑148 (MQ=255)                                                                                             aggACTCTTTTTGTGTAATGACGGAGTTCACATTTTTAATTT‑AGATAAAAGGAGAAAAAAAAAGAAAAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGc                                                    <  2:505698/147‑1 (MQ=255)                                                                                              tgattttttttGTGAAATGACGGA‑CTCCGATTTTTAATTTAAGAAAAAGGGGAAAAAAAAAAACAAAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGAt                                                      <  1:753629/140‑1 (MQ=255)                                                                                              tGACATTTTTTGTGAAATGAGGGATTTCATTTTTTAAATTA‑AAAACAAAGGAGAAAAAAAAAGAAAAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCa                                                  <  1:518458/150‑1 (MQ=255)                                                                                              tGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTT‑AGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCAt                                                 >  2:850313/1‑151 (MQ=255)                                                                                                  acTTTTTGTGTAATGACGGAGTTCACATTTTTAATTT‑AGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGc                                             >  2:169405/1‑151 (MQ=255)                                                                                                     ttttGTGAAATGAGGGAGTTCACTTTTTTAATTT‑AGAAAAAAGGAGGAAAAAAAAGAAAAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAg                                           <  1:150347/150‑1 (MQ=255)                                                                                                      tttGTGAAATGAGGGATTTCAAATTTTTAATTA‑AAATAAAAGGAGAAAAAAAAAGAAAAAAAACCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGc                                          <  1:884511/150‑1 (MQ=255)                                                                                                      tttGTGAAATGACGGATTTCACATTTTTAATTT‑AGAAAAAAGGAGAAAAAAAAAAAAAAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGc                                          <  1:387237/150‑1 (MQ=255)                                                                                                        tgtgTAATGACGGAGTTCACATTTTTAATTT‑AGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGt                                        >  2:342218/1‑150 (MQ=255)                                                                                                             aaggggggATTTCAATTTTTTAATTA‑AAAAAAAAGGAGAAAAAAAAAGAAAAAAAACCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGa                                     <  1:556063/142‑1 (MQ=255)                                                                                                             aaTGCCGGATTTCATTTTTTTAATTA‑AGAAAAAAGGAGAAAAAAAAAGAAAAAAAACCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAg                                   <  1:333594/150‑1 (MQ=255)                                                                                                                 aCGGAGTTCACATTTTTAATTT‑AGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTc                              >  2:482858/1‑151 (MQ=255)                                                                                                                   ggAGTTCACATTTTTAATTT‑AGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCAt                            >  1:517835/1‑151 (MQ=255)                                                                                                                     aGTTCACATTTTTAATTT‑AGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGACATCt                          >  2:97673/1‑151 (MQ=255)                                                                                                                      gTTCACATTTTTAATTT‑AGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCtt                         >  1:965281/1‑151 (MQ=255)                                                                                                                        tCACATTTTTAATTT‑AGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTc                        >  2:353940/1‑150 (MQ=255)                                                                                                                          ataTTTTAAATTT‑AGATAAAGGGGGAAAAAAAAACCAAAAAAACCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCa                       <  1:683490/147‑1 (MQ=255)                                                                                                                             tttttAATTT‑AGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCa                   >  2:807453/1‑150 (MQ=255)                                                                                                                             tttttAATTA‑AAAAAAAAGGAGAAAAAAAAAGAAAAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATcc                    <  2:41835/149‑1 (MQ=255)                                                                                                                                ttaatta‑aGATAAAGGGAGAAAAAAAAAGAAAAAAAACCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACa                <  1:757493/150‑1 (MQ=255)                                                                                                                                ttaatta‑aGAACAAAGGAGGAATAAAAGGAAAAAAAGGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAAc                 <  1:891073/149‑1 (MQ=255)                                                                                                                                  aaTTA‑AGAAAAAGGGAGAAAAAAAAAGAAAAAAAACCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAgg              <  1:177942/150‑1 (MQ=255)                                                                                                                                        agacaaagggagaaAAAAAAAGAAAAAAAACCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGAtt        <  1:122073/143‑1 (MQ=255)                                                                                                                                            cAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTtat    >  2:416788/1‑151 (MQ=255)                                                                                                                                              aaGGAGAAAGAATAAGAAAAAAAACCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTATAg  <  1:10062/151‑1 (MQ=255)                                                                                                                                              aaGGAGAAAAAAAAAGCAAAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTATAg  <  1:532507/151‑1 (MQ=255)                                                                                                                                                       |                                                                                                                                              AGTTAATTCTGAATCGGAAATATCGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTT‑AGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTATAG  >  NC_000913/1435569‑1435859

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: ‑