Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,356,201	0	T	G	54.2%	54.3 / 70.6	49	T304P (ACC→CCC)	sapA	antimicrobial peptide transport ABC transporter periplasmic binding protein
Reads supporting (aligned to +/- strand):  ref base T (6/16);  new base G (26/0);  total (33/16)
Fisher's exact test for biased strand distribution p-value = 3.31e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.18e-07

CGTTGTCATAGGCCCACGAGGCGCGCGGTAAAATAGAGGCCGCCGTTTCAGCCGTACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGG‑TTTGGCGGTGTTAAATGCCAGATAGGCGACGTTCATCCCAGGA‑CGCAG‑CGTTAAACGCAAGCGCGGGTCGTCACG‑CAAAATGGATAGCTGGCTGG‑CAGCAGGCCAGGCCAGAACGTCGCATTCCCCGGTCAGGAGTTTCGACAGACGTCCGGTGCCGCC  >  NC_000913/1356054‑1356351                                                                                                                                                     |                                                                                                                                                           cGTTGTCATAGGCCCACGAGGCGCGCGGTAAAATAGAGGCCGCCGTTTCAGCCGTACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGG‑TTTGGCGgtg                                                                                                                                                           <  1:556579/149‑1 (MQ=255)    tGTCATAGGCCCACGAGGCGCGCGGTAAAATAGAGGCCGCCGTTTCAGCCGTACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGG‑CTTGGGGGGGTTaa                                                                                                                                                       >  2:314153/1‑150 (MQ=255)           ggCCCACGAGGCGCGCGGTAAAATAGAGGCCGCCGTTTCAGCCGTACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGG‑TTTTGCGGGGGTAAATGcc                                                                                                                                                  >  1:634822/1‑148 (MQ=255)              ccACGAGGCGCGCGGTAAAATAGAGGCCGCCGTTTCAGCCGTACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGG‑TTTGGCGGTGTTAAATGCCAGATAg                                                                                                                                            <  1:697624/151‑1 (MQ=255)              ccACGAGGCGCGCGGTAAAATAGAGGCCGCCGTTTCAGCCGTACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGG‑TTTGGCGGTGTTAAATGCCAGATAg                                                                                                                                            <  2:419137/151‑1 (MQ=255)               cACGAGGCGCGCGGTAAAATAGAGGCCGCCGTTTCAGCCGTACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGG‑TTTTGCGGGGTTTAAAGCCAGAAAgg                                                                                                                                           >  2:599984/1‑151 (MQ=255)               cACGAGGCGCGCGGTAAAATAGAGGCCGCCGTTTCAGCCGTACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGG‑TTTTGCGGGGTTAAATGCCAGATAgg                                                                                                                                           >  2:20403/1‑151 (MQ=255)                  gAGGCGCGCGGTAAAATAGAGGCCGCCGTTTCAGCCGTACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGG‑TTTGGCGGGGGTAAAAGCCAGATAGGCg                                                                                                                                         >  2:446459/1‑150 (MQ=255)                      cgcgcgGTAAAATAGAGGCCGCCGTTTCAGCCGTACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGG‑TTTGGCGGTGTTAAATGCCAGATAGGCGACGtt                                                                                                                                    <  2:222071/151‑1 (MQ=255)                        cgcgGTAAAATAGAGGCCGCCGTTTCAGCCGTACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGG‑TTTGGCGGTGTTAAATGCCAGATAGGCGACGTTCa                                                                                                                                  <  1:506017/151‑1 (MQ=255)                          cgGTAAAATAGAGGCCGCCGTTTCAGCCGTACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGG‑TTTTGGGGTGGTTAAAGCCAAATAGGCGaaggtc                                                                                                                                   >  1:801778/1‑143 (MQ=255)                          cgGAAAAATAGAGGCCGCCGTTTCAGCCGTACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGG‑CTTGGCGGAGTTCAAAGACAGATaaaggaacttc                                                                                                                                   >  2:104361/1‑138 (MQ=255)                            gTAAAATAGAGGCCGCCGTTTCAGCCGTACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGG‑GTTGGGGGGGGTCAAAGCCACGTAAGCGGCGGTCAttc                                                                                                                               >  1:661890/1‑148 (MQ=255)                                            cgTTTCAGCCGTACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGG‑TTTTGCGGGGTTTAAATCCAGAAAGGCGGCGTTTATCCCCCGA‑CGCAggggtta                                                                                                              >  1:711144/1‑144 (MQ=255)                                            cgTTTCAGCCGTACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGG‑TTTTGCGGGGGTTAAAACCAGATAAGCGGAGCTTATCCCCGGA‑CGCAG‑Cggtta                                                                                                             >  1:38605/1‑146 (MQ=255)                                             gTTTCAGCCGTACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGG‑TTTGGCGGTGTTAAATGCCAGATAGGCGACGTTCATCCCAGGA‑CGCAG‑CGTTAAAc                                                                                                           <  2:613792/151‑1 (MQ=255)                                              tttCAGCCGTACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGG‑TTTTGCGGGGGTAAAAGCCAGATAGGGGACGTTCATCCCCGGA‑CGCAG‑CGTTaaa                                                                                                            >  2:112225/1‑149 (MQ=255)                                                tCAGCAGTACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGG‑TTTTGGGGGGTTAAAAGCCACAAAAGCGACGGTCATCCCCGGG‑CCCAG‑Cgcttaa                                                                                                            >  1:672536/1‑142 (MQ=255)                                                  aGCCGTACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGG‑TTTGGCGGGGGTAAATGCCAGACAGGGGACGGTCATCCCAGGA‑CCCAG‑CGTTAAACGcca                                                                                                       >  2:821246/1‑148 (MQ=255)                                                    ccGTACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGG‑TTTGGCGGTGGTTAAAGTCAAAAAAGCGACGGTTATCCCAAGA‑CGGAG‑CGGTTAACGCaa                                                                                                       >  1:702173/1‑148 (MQ=255)                                                     cGTACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGG‑ATTGGCGGGGCTAAAAGCCAGACAAGCGGCGTTTATCCCCGGA‑CACAG‑CGATAAACCCCAgc                                                                                                     >  2:624057/1‑149 (MQ=255)                                                        aCCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGG‑TTTGGCGGTGTTAAATGCCAGATAGGCGACGTTCATCCCAGGA‑CGCAG‑CGTTAAACGCAAGCGCgg                                                                                                 <  2:594617/150‑1 (MQ=255)                                                            taataGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGG‑TTTGGCGGGGTTTAAAGCCCCAAAAGCGGCGGTTATCCCCGGA‑CGCAG‑CGGTAAAACCAAGCCCgggg                                                                                               >  1:779096/1‑147 (MQ=255)                                                                   tGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGG‑TTTGGCGGGGGTAAATGCCAGATAAGCGGCGGTCATCCCCGGA‑CGCAG‑CGGTTAAAGCAAGCGCGGGGCGGCAc                                                                                         >  2:154563/1‑147 (MQ=255)                                                                       ttGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGGTTTTGGGGGGGTTAAA‑GCCCGATAAGGGCGGCTCATCCCCTGACCCCAC‑CGTTAACCCCAAG‑GCGGGTCGTCAcc                                                                                        >  2:706282/1‑143 (MQ=255)                                                                          cATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGG‑TTTTGCGGGGTTAAATGCCAGAAAAGCGCCGTTCAACCCCGGA‑CCCAGACGTT‑AACGCCAACGCCGGGGGTCACG‑CAAAAggg                                                                               >  1:285976/1‑149 (MQ=255)                                                                          cATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGG‑TTTTGCGGGGTTAAAAGCCAAATAAGGGACGGTCATCCCAAGG‑CGCAG‑CGGTAAAAGCAAACGCGGGGCGGCACG‑Ccaaa                                                                                  >  1:928462/1‑146 (MQ=255)                                                                          cATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGG‑TTTGGCGGTGTTAAATGCCAGATAGGCGACGTTCATCCCAGGA‑CGCAG‑CGTTAAACGCAAGCGCGGGTCGTCACG‑CAAAATGGAt                                                                             <  2:500675/151‑1 (MQ=255)                                                                          cATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGG‑TTTGGCGGTGTTAAATGCCAGATAGGCGACGTTCATCCCAGGA‑CGCAG‑CGTTAAACGCAAGCGCGGGTCGTCACG‑CAAAATGGAt                                                                             <  2:634678/151‑1 (MQ=255)                                                                             cAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGG‑TTTGGCGGTGTTAAATGCCAGATAGGCGACGTTCATCCCAGGA‑CGCAG‑CGTTAAACGCAAGCGCGGGTCGTCACG‑CAAAATGGATAgc                                                                          <  2:517827/151‑1 (MQ=255)                                                                             cAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGG‑TTTGGCGGTGTTAAATGCCAGATAGGCGACGTTCATCCCAGGA‑CGCAG‑CGTTAAACGCAAGCGCGGGTCGTCACG‑CAAAATGGATAg                                                                           <  1:208803/150‑1 (MQ=255)                                                                                  gcTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGG‑TTTGGGGGGGTTTAAAGCCAGATAAGCGGCGGTCATCCCCGGA‑CGCAG‑CGGTTAAAGCAAACGCGGGGCGGCACG‑CAAAAAgggaa                                                                            >  1:412942/1‑141 (MQ=255)                                                                                    tGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGG‑TTTGGCGGGGTTAAAAGCCAGATAGGCGGCGTTCATCCCAGGA‑CGCAG‑CGTTTAAAGCAAACGCGGGTCGTCACG‑CAAAAAGGAAAGcttggtgg                                                                   >  1:196324/1‑151 (MQ=255)                                                                                           taATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGG‑TTTTGCGGGGTTAAATGCCCGAAAGGCGGCGTTCATCCCCGGA‑CCCAG‑CGGTAAAAGCAAGCGCGGGGCGTCACG‑CAAAATTGATAgctggctg                                                                    >  2:187421/1‑143 (MQ=255)                                                                                            aaTCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGG‑TTTGGCGGTGTTAAATGCCAGATAGGCGACGTTCATCCCAGGA‑CGCAG‑CGTTAAACGCAAGCGCGGGTCGTCACG‑CAAAATGGATAGCTGGCTGG‑CAGcaggc                                                          <  1:879486/151‑1 (MQ=255)                                                                                            aaTCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGG‑TTTGGCGGTGTTAAATGCCAGATAGGCGACGTTCATCCCAGGA‑CGCAG‑CGTTAAACGCAAGCGCGGGTCGTCACG‑CAAAATGGATAGCTGGCTGG‑CAGcagg                                                           <  1:844276/150‑1 (MQ=255)                                                                                                 ccAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGG‑TTTGGGGGTGGTAAATTCCCAATAAGCGACGTTCATTCCAGGA‑CGCAG‑CGTTAAACGCAAGCGCGGGGCGGCACG‑CAAAATGGATAGCTGGCCGG‑CAGcaggccagg                                                      >  2:125116/1‑150 (MQ=255)                                                                                                    gTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGG‑TTTGGCGGGGTTAAATGCCCGAAAGGGGGCGGTTATCCCCCGA‑CGCCG‑CGGTAAAAGCAAACGCGGGGCGTCACG‑CAAAAAGGGAAACTGGGTGG‑CAGCaggcccggcc                                                    >  1:144466/1‑149 (MQ=255)                                                                                                     tGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGG‑TTTGGCGGGGGTAAATGCCAGAAAGGCGGCGTTTATCCCCGGA‑CGCCG‑CGGTTAACGCAAGCGCGGGGCGTCACG‑CAAAAAGGATAGCTGGCTGG‑CAGcagggccgggc                                                    >  1:358099/1‑141 (MQ=255)                                                                                                           cgcATGGCGGACAGCGGGATTATTTAGCGGCGG‑TTTTGCGGTGTTAAATGCCAGATAGGCGGCGTTTATCCCCGGA‑CGCAG‑CGGTTAAAGCAAGCGCGGGGGGTCACG‑CCAAATGGATAGCTGGGTGG‑CAGCAGGCCCGGCCCGAACGGCg                                           >  2:835784/1‑151 (MQ=255)                                                                                                             cATGGCGGACAGCGGGATTATTTAGCGGCGG‑TTTGGCGGTGTTAAATGCCAGATAGGCGACGTTCATCCCAGGA‑CGCAG‑CGTTAAACGCAAGCGCGGGTCGTCACG‑CAAAATGGATAGCTGGCTGG‑CAGCAGGCCAGGCCAGAACGTCGCa                                         <  2:94285/151‑1 (MQ=255)                                                                                                                   ggACAGCGGGATTATTTAGCGGCGGTTTTGGGGGGGTTAATTG‑CAAATAAGGGGCGGTTATTCCAGGA‑CGCAG‑CGGTTAAAGCAAAGGCGGGGCGGCACG‑CAAAATGGATAACTGGGCGG‑GGGCAGGGCAGGCCCAAACATCGCCATcccc                                   >  1:683317/1‑151 (MQ=255)                                                                                                                     aCAGCGGGATTATTTAGCGGCGG‑TTTTGTGGGGTTTAAAACCAAATAAGGGACGGTCATACCCGGA‑CGCAA‑CGTTTAAAGCAAACGCGGGGGGTCCCGCCAAAATGG‑GAGCTGGGTTG‑CAGGAAGGCAAGCCAGGACgacccctttccc                                   >  2:820645/1‑138 (MQ=255)                                                                                                                        gCGGGATTATTTAGCGGCGG‑TTTGGCGGTGTTAAATGCCAGATAGGCGACGTTCATCCCAGGA‑CGCAG‑CGTTAAACGCAAGCGCGGGTCGTCACG‑CAAAATGGATAGCTGGCTGG‑CAGCAGGCCAGGCCAGAACGTCGCATTCCCCGGTCa                              <  1:414713/151‑1 (MQ=255)                                                                                                                         cGGGATTATTTAGCGGCGGTTTTGGGGGGGTTAAA‑GCCAGAAAGGCGGCGTTTATCCCCGGA‑CGCAG‑CGTTTAAAACAAGCGGGGGGCGTCCCC‑CAAAATTGATAAGTGGCTGGCCACCAGGCCGGGCACAAACG‑CGCACTcccc                                   >  1:783734/1‑145 (MQ=255)                                                                                                                                attTAGCGGCGG‑TTTGGCGGTGTTAAATGCCAGATAGGCGACGTTCATCCCAGGA‑CGCAG‑CGTTAAACGCAAGCGCGGGTCGTCACG‑CAAAATGGATAGCTGGCTGG‑CAGCAGGCCAGGCCAGAACGTCGCATTCCCCGGTCAGGAGTTTc                      <  2:634833/151‑1 (MQ=255)                                                                                                                                   tAGCGGCGG‑TTTGGCGGTGTTAAATGCCAGATAGGCGACGTTCATCCCAGGA‑CGCAG‑CGTTAAACGCAAGCGCGGGTCGTCACG‑CAAAATGGATAGCTGGCTGG‑CAGCAGGCCAGGCCAGAACGTCGCATTCCCCGGTCAGGAGTTTCGa                    <  2:771252/150‑1 (MQ=255)                                                                                                                                      cggcgg‑TTTGGCGGGGTTAAATGCCAGATAGGCGACGTTCATCCCAGGA‑CGCAG‑CGTTAAACGCAAGCGCGGGGCGTCACG‑CAAAATGGATAGCTGGCTGG‑CAGCAGGCCAGGCCAGAACGTCGCATTCCCCGGTCAGGAGTTTCGAc                   >  2:243010/1‑148 (MQ=255)                                                                                                                                       ggcgg‑TTTGGCGGTGTTAAATGCCAGATAGGCGACGTTCATCCCAGGA‑CGCAG‑CGTTAAACGCAAGCGCGGGTCGTCACG‑CAAAATGGATAGCTGGCTGG‑CAGCAGGCCAGGCCAGAACGTCGCATTCCCCGGTCAGGAGTTTCGACAGAc               >  1:237686/1‑151 (MQ=255)                                                                                                                                           g‑TTTGGCGGTGTTAAATGCCAGATAGGCGACGTTCATCCCAGGA‑CGCAG‑CGTTAAACGCAAGCGCGGGTCGTCACG‑CAAAATGGATAGCTGGCTGG‑CAGCAGGCCAGGCCAGAACGTCGCATTCCCCGGTCAGGAGTTTCGACAGACGTcc           >  1:752546/1‑151 (MQ=255)                                                                                                                                                     tgtTAAATGCCAGATAGGCGACGTTCATCCCAGGA‑CGCAG‑CGTTAAACGCAAGCGCGGGTCGTCACG‑CAAAATGGATAGCTGGCTGG‑CAGCAGGCCAGGCCAGAACGTCGCATTCCCCGGTCAGGAGTTTCGACAGACGTCCGGTgccgcc  >  2:9714/1‑151 (MQ=255)                                                                                                                                                     |                                                                                                                                                           CGTTGTCATAGGCCCACGAGGCGCGCGGTAAAATAGAGGCCGCCGTTTCAGCCGTACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGG‑TTTGGCGGTGTTAAATGCCAGATAGGCGACGTTCATCCCAGGA‑CGCAG‑CGTTAAACGCAAGCGCGGGTCGTCACG‑CAAAATGGATAGCTGGCTGG‑CAGCAGGCCAGGCCAGAACGTCGCATTCCCCGGTCAGGAGTTTCGACAGACGTCCGGTGCCGCC  >  NC_000913/1356054‑1356351

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑