Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	987,494	0	T	G	43.1%	83.3 / 15.1	51	intergenic (‑512/+91)	ompF/asnS	outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase
Reads supporting (aligned to +/- strand):  ref base T (2/27);  new base G (22/0);  total (24/27)
Fisher's exact test for biased strand distribution p-value = 1.77e-12
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTCAGACATCCAGAATGCCAAAAAATAGTATGAAAATTGTGCTATTAGCTAAGAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGTTG‑CAAATAGATTGCTTGAC‑TT‑AACAAACAGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTAAATTAGAAGCTGGCGTTACGCGGAGTACGTGGGAACGGAATCACATCACGTACGTTTTGCAC  >  NC_000913/987349‑987644                                                                                                                                                   |                                                                                                                                                          ttCAGACATCCAGAATGCCAAAAAATAGTATGAAAATTGTGCTATTAGCTAAGAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGTTG‑Ca                                                                                                                                                      <  1:443829/150‑1 (MQ=255)   cAGACATCCAGAATGCCAAAAAATAGTATGAAAATTGTGCTATTAGCTAAGAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGGTG‑Gaaa                                                                                                                                                    >  2:871049/1‑150 (MQ=255)    aGACATCCAGAATGCCAAAAAATAGTATGAAAATTGTGCTATTAGCTAAGAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGTTG‑CAAATa                                                                                                                                                  <  1:210262/151‑1 (MQ=255)        aTCCAGAATGCCAAAAAATAGTATGAAAATTGTGCTATTAGCTAAGAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGTTG‑CAAATAGAtt                                                                                                                                              <  1:921029/151‑1 (MQ=255)            aGAATGCCAAAAAATAGTATGAAAATTGTGCTATTAGCTAAGAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGTTG‑CAAATAGATTGCtt                                                                                                                                          <  2:917500/151‑1 (MQ=255)             gAATGCCAAAAAATAGTATGAAAATTGTGCTATTAGCTAAGAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGTTG‑CAAATAGATTGCTTg                                                                                                                                         <  1:629644/151‑1 (MQ=255)                     aaaaaTAGTATGAAAATTGTGCTATTAGCTAAGAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGGTG‑GAAAAAAATTGCtttttttaa                                                                                                                                   >  1:895176/1‑142 (MQ=255)                             tATGAAAATTGTGCTATTAGCTAAGAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGGTG‑GCAATAAATTGCTTTAT‑TT‑tacaaacaaa                                                                                                                         >  2:529551/1‑147 (MQ=255)                              aTGAAAATTGTGCTATTAGCTAAGAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGTTG‑CAAATAGATTGCTTGAC‑TT‑AACAAACAGATaa                                                                                                                      <  2:256206/151‑1 (MQ=255)                              aTGAAAATTGTGCTATTAGCTAAGAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGTTG‑CAAATAGATTGCTTGAC‑TT‑AACAAACAGATaa                                                                                                                      <  1:131033/151‑1 (MQ=255)                              aTGAAAATTGTGCTATTAGCTAAGAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGTTG‑CAAATAGATTGCTTGAC‑TT‑AACAAACAGATa                                                                                                                       <  2:721739/150‑1 (MQ=255)                                  aaaTTGTGCTATTAGCTAAGAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGTTG‑CAAATAGATTGCTTGAC‑TT‑AACAAACAGATAACTTg                                                                                                                  <  2:673233/151‑1 (MQ=255)                                       gtgCTATTAGCTAAGAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGTTG‑CAAATAGATTGCTTGAC‑TT‑AACAAACAGATAACTTGACAg                                                                                                              <  2:606653/150‑1 (MQ=255)                                             ttAGCTAAGAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGGTG‑GAAAAAGAATGGTTGAA‑TT‑TAAAAAAAAAAAAATTTAAAGaaaa                                                                                                          >  2:534287/1‑148 (MQ=255)                                             ttAGCTAAGAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGGTG‑CAAAAAAATTGCTTTTC‑TT‑AAAAAAAAAAAAAATTTAAAGaaaaaa                                                                                                        >  2:848026/1‑148 (MQ=255)                                               aGCTAAGAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGGTG‑CAAAAAAAATGCTTTAC‑TT‑TAAAAAAAAAAAAATTGACAGaaaaaaaa                                                                                                      >  2:502088/1‑146 (MQ=255)                                                         aaaCTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGGTG‑GAAAAAAATTTGTTGTA‑TT‑TAAAAACAAAAAAAATTAAAGGAAAGAaaaaaaaa                                                                                                >  1:59548/1‑146 (MQ=255)                                                          aaCTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGGTG‑CAAAAAAATTTTTTTAC‑TT‑TAAAAAAAAAAAACATGACAGAAAAGAaaaaaaaaaa                                                                                              >  1:890056/1‑145 (MQ=255)                                                              aaTCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGTTG‑CAAATAGATTGCTTGAC‑TT‑AACAAACAGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGc                                                                                        <  1:554496/149‑1 (MQ=255)                                                                  cGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGGTG‑GCAAAAAAATGCTTGAC‑TT‑TACAAAAAAAAAAATTTACAAAAAAAATAAAAAAAAAAACAGCGGgcg                                                                                   >  2:501900/1‑150 (MQ=255)                                                                   gCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGGTG‑CAAAAAGATTGCTTGAC‑TT‑AACAAAAAAAAAAATTGTCAGAAAAAAAAAAAAAAAAAACAGCGGgcg                                                                                   >  2:558087/1‑149 (MQ=255)                                                                    cAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGTTG‑CAAATAGATTGCTTGAC‑TT‑AACAAACAGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTg                                                                                <  1:213024/151‑1 (MQ=255)                                                                        aaGAATGCGGATTATTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGTTG‑CAAATAGATTGCTTGAC‑TT‑AACAAACAGATAACTTGCCAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGct                                                                             <  1:503104/150‑1 (MQ=255)                                                                          gAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGTTG‑CAAATAGATTGCTTGAC‑TT‑AACAAACAGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCtt                                                                          <  2:702602/151‑1 (MQ=255)                                                                          gAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGGTG‑GAAAAAAATTTCTTTAC‑TT‑TAAAAAAAAAAAACTTGACAGAAAAAAAAAAAAAAAAAACAACGGGCGCTGGGTCtt                                                                          >  2:736430/1‑151 (MQ=255)                                                                           aaTGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGGTTG‑GAAA‑AGAATGTTTTAG‑TT‑TACAAAAAAAAAAAATTAAAGAAAAGAAAAAAAAAAAAACAGCGGGCGGTgg                                                                               >  1:877613/1‑145 (MQ=255)                                                                           aaTGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGGTG‑CAAAAAGAATGCTTGAC‑TT‑TACAAAAAAAAAAATTGTCAGAAAAAAAAAAAAAAAAAACAGCGGGCGCCGGctc                                                                            >  2:876319/1‑148 (MQ=255)                                                                              gCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGTTG‑CAAATAGATTGCTTGAC‑TT‑AACAAACAGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAg                                                                      <  2:686985/151‑1 (MQ=255)                                                                              gCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGGTG‑TAAAAAGAATTTTTGGCTTT‑AAAAAAAAAAAAAATTAAC‑GAAAAGAAAAAAAAAAAAACAACGGGGGCCGGGTCTTgta                                                                       >  2:405498/1‑148 (MQ=255)                                                                                ggATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGGTG‑CAAAAAAAATGCTTTGC‑TT‑AAAAAACAAATAACTTGAAAAAAAAAATAAAAAAAAAGCCAACGGGCGGGGGCCCttcta                                                                       >  2:214413/1‑145 (MQ=255)                                                                                        ttttGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGGTG‑GAAATAAAATTTTTGAT‑TT‑AACAAAAAGAGAAATTGAAAGAAAAAAAAAAAAAAAAAACAGAGGGGGCTGGCTCCTGAAGACACCAAAtt                                                            >  2:538955/1‑151 (MQ=255)                                                                                         tttGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGTTG‑CAAATAGATTGCTTGAC‑TT‑AACAAACAGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTAAAtt                                                            <  1:198880/150‑1 (MQ=255)                                                                                            gcgcGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGGTG‑CCAATAAAATGGTTGGC‑TT‑TATAAAAACATAAATTTTCAAAAAAAAAAAAAAAAAAAGCAACGGGCGCCGGGTCtttgagaacccaaa                                                              >  2:415554/1‑133 (MQ=255)                                                                                                      gTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGTTG‑CAAATAGATTGCTTGAC‑TT‑AACAAACAGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTAAATTAGAAGCTGGCGtt                                               <  1:744130/150‑1 (MQ=255)                                                                                                      gTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGGTG‑GAAAAAAATTTCTTTTC‑TTAAAAAAAAAAAAAATTTGAC‑GAAAAAAAAAAAAAAAAAGAAACGGGGGGTGGGTCTTGTAGAAGCTAAAATAAAAACTGGCGtt                                               >  1:859628/1‑150 (MQ=255)                                                                                                       ttGCAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGTTG‑CAAATAGATTGCTTGAC‑TT‑AACAAACAGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTAAATTAGAAGCTGGCGTTa                                              <  1:751861/150‑1 (MQ=255)                                                                                                        tGCAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGGTG‑TAAAAAAATTTTTTTAC‑TT‑TAAAAAAAAAAAAAATTTCAGAAAAAAAAAAAAAAAAAACAGCGGGGGGCGGCTCTTTAAGAAGCAAAAATaaaaaaaagcggtacg                                            >  1:700414/1‑139 (MQ=255)                                                                                                         gCAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGTTG‑CAAATAGATTGCTTGAC‑TT‑AACAAACAGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTAAATTAGAAGCTGGCGTTAcgc                                           <  1:305026/151‑1 (MQ=255)                                                                                                          cAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGGTGTGAAAAAATTTGTTTGA‑‑TT‑AACAAAAAGATAAATTTAGAGGAAAAAAAAAAAAAAAGACACCGGGCGGCGGGTCTTTTAGACGAGAAAATAGaaaaatgcggt                                               >  1:472645/1‑137 (MQ=255)                                                                                                               tAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGGTG‑CAAAAAAAATGCTTTAC‑TT‑TACAAAAAGATAACTTTACAGAAAAAATAAAAAAAAAACCAGCGGGGGCTGGCTCTTTTAGAAGCTAAATTAAAAACTGGGGGTACGCGGAGt                                      >  2:476198/1‑150 (MQ=255)                                                                                                                       cGTAACAGGATGATCGTTATGGC‑GGGGGTG‑CAAAAAGATTGCTTGAC‑TT‑AACAAAAAGATAACTTTACAGAAAAGATAAAAAAAAAAACAGCGGGGGCCGGCTCCTGAAGACGCCAAATTAGAAGCTGGGGGTACGCCGAGTACGTggg                               >  2:422626/1‑149 (MQ=255)                                                                                                                        gTAACAGGATGATCGTTATGGC‑GGGGTTG‑CAAATAGATTGCTTGAC‑TT‑AACAAACAGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTAAATTAGAAGCTGGCGTTACGCGGAGTACGTGGGAAc                            <  1:484974/151‑1 (MQ=255)                                                                                                                        gTAACAGGATGATCGTTATGGC‑GGGGTTG‑CAAATAGATTGCTTGAC‑TT‑AACAAACAGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTAAATTAGAAGCTGGCGTTACGCGGAGTACGTGGGAAc                            <  1:479887/151‑1 (MQ=255)                                                                                                                          aaCAGGATGATCGTTATGGC‑GGGGTTG‑CAAATAGATTGCTTGAC‑TT‑AACAAACAGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTAAATTAGAAGCTGGCGTTACGCGGAGTACGTGGGAACgg                          <  2:354377/151‑1 (MQ=255)                                                                                                                           aCAGGATGATCGTTATGGC‑GGGGGTG‑GAAATAAATTGGTTTGT‑TT‑AAAAAAAAGAAAAATTGAAAGAAAAAAAAAAAAAAAAAGCAGCGGGGGCGGGGTCTTTGAAAAGGTAAAATAGAAGGAGGGGGTATGCGGAATACGgggggaag                           >  2:759413/1‑145 (MQ=255)                                                                                                                              ggATGATCGTTATGGC‑GGGGTTG‑CAAATAGATTGCTTGAC‑TT‑AACAAACAGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTAAATTAGAAGCTGGCGTTACGCGGAGTACGTGGGAACGGAatc                      <  1:148949/151‑1 (MQ=255)                                                                                                                               gatgatCGTTATGGC‑GGGGTTG‑CAAATAGATTGCTTGAC‑TT‑AACAAACAGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTAAATTAGAAGCTGGCGTTACGCGGAGTACGTGGGAACGGAatca                     <  2:189599/151‑1 (MQ=255)                                                                                                                                      gTTATGGC‑GGGGTTG‑CAAATAGATTGCTTGAC‑TT‑AACAAACAGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTAAATTAGAAGCTGGCGTTACGCGGAGTACGTGGGAACGGAATCACATCacg              <  1:843443/151‑1 (MQ=255)                                                                                                                                         aTGGC‑GGGGTTG‑CAAATAGATTGCTTGAC‑TT‑AACAAACAGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTAAATTAGAAGCTGGCGTTACGCGGAGTACGTGGGAACGGAATCACATCacgtac           <  1:402339/151‑1 (MQ=255)                                                                                                                                           ggC‑GGGGTTG‑CAAATAGATTGCTTGAC‑TT‑AACAAACAGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTAAATTAGAAGCTGGCGTTACGCGGAGTACGTGGGAACGGAATCACATCacgtacg          <  2:751433/150‑1 (MQ=255)                                                                                                                                             c‑GGGGTTG‑CAAATAGATTGCTTGAC‑TT‑AACAAACAGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTAAATTAGAAGCTGGCGTTACGCGGAGTACGTGGGAACGGAATCACATCACGTACGttt       >  2:639125/1‑151 (MQ=255)                                                                                                                                                   ttG‑CAAATAGATTGCTTGAC‑TT‑AACAAACAGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTAAATTAGAAGCTGGCGTTACGCGGAGTACGTGGGAACGGAATCACATCACGTACGTTTTGCAc  >  2:392190/1‑151 (MQ=255)                                                                                                                                                   |                                                                                                                                                          TTCAGACATCCAGAATGCCAAAAAATAGTATGAAAATTGTGCTATTAGCTAAGAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGTTG‑CAAATAGATTGCTTGAC‑TT‑AACAAACAGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTAAATTAGAAGCTGGCGTTACGCGGAGTACGTGGGAACGGAATCACATCACGTACGTTTTGCAC  >  NC_000913/987349‑987644

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑