Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913987,4940TG56.0% 24.0 / 35.7 26intergenic (‑512/+91)ompF/asnSouter membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase
Reads supporting (aligned to +/- strand):  ref base T (2/9);  new base G (14/0);  total (17/9)
Fisher's exact test for biased strand distribution p-value = 2.69e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.79e-05

GAATGCCAAAAAATAGTATGAAAATTGTGCTATTAGCTAAGAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGTTGCAAATAGATTGCTTGACTTAACAAACAGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTAAATTAGAAGCTGGCGTTACGCGGAGTACGTGGGAACGGAATCACATCACGTACGTTTTGCA  >  NC_000913/987361‑987643
                                                                                                                                     |                                                                                                                                                     
gAATGCCAAAAAATAGTATGAAAATTGTGCTATTAGCTAAGAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGGTGCAAATAAAtttttt                                                                                                                                       >  1:475653/1‑146 (MQ=255)
     ccAAAAAATAGTATGAAAATTGTGCTATTAGCTAAGAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGGTGCAAAAAGATTTTTTTACtt                                                                                                                                  >  2:334202/1‑150 (MQ=255)
                   gAAAATTGTGCTATTAGCTAAGAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGGTGCAAATAAAATGGTTTAATTaacaaaaaaaaaaat                                                                                                                   >  1:489840/1‑142 (MQ=255)
                                      aaGAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGTTGCAAATAGATTGCTTGACTTAACAAACAGATAACTTGACAGAAAAGATaaaaaa                                                                                                <  2:475631/151‑1 (MQ=255)
                                        gAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGTTGCAAATAGATTGCTTGACTTAACAAACAGATAACTTGACAGAAAAGATaaaaaa                                                                                                <  1:568867/149‑1 (MQ=255)
                                        gAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGGTGGAAAAAAAATTGTTTACTTTACAAAAAAAAAAAATGACAGaaaaaaaaaaaaaa                                                                                               >  2:620767/1‑150 (MQ=255)
                                         aaaaaaCTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGGTGTAAAAAAAATTGTTTACTTAACAAAAAAAAAAATTTaaaaaaaaaaaaaaaaaaa                                                                                              >  2:653613/1‑149 (MQ=255)
                                             aaCTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGGTGGAAAAAAAATTCTTGACTTAAAAAACAAAAAAATTTTTCAAAAAAATaaaaaaaaa                                                                                             >  1:336039/1‑145 (MQ=255)
                                                 aaTCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGTTGCAAATAGATTGCTTGACTTAACAAACAGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCgg                                                                                     <  1:390060/151‑1 (MQ=255)
                                                  aTCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGGTGGAAATAGATTTCTTTTCTTTAAAAAAAAAAAAATTTACAGAAAAAAAAAAAAAAAAACCAGCggg                                                                                    >  1:302854/1‑151 (MQ=255)
                                                     cGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGGTGCAAAAAAAATGCTTGACTTTACAAAAAGAAAAATTGACAGAAAAGATAAAAAAAAAAACAGCggg                                                                                    >  1:482709/1‑148 (MQ=255)
                                                       cAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGTTGCAAATAGATTGCTTGACTTAACAAACAGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTg                                                                               <  2:558475/151‑1 (MQ=255)
                                                                      ttAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGGTGCAAAAAAAATTCTTTACTTTAAAAAAAAAAAAATTTACAGAAAAAAAAAAAAAAAAAACAGCGGGCGCCGGCTCCTGAAGaa                                                                   >  1:328175/1‑147 (MQ=255)
                                                                        aGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGTTGCAAATAGATTGCTTGACTTAACAAACAGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTaa                                                              <  1:620804/151‑1 (MQ=255)
                                                                         gTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGATGCGAAAAAAATGTCTGATTTAACAAAAAAATAAATTGTAAGAAAAAATAAAAAAAAAGACAGCGGGGGGGGGGTCTTTAAGaggaaaa                                                              >  1:652862/1‑144 (MQ=255)
                                                                                cgcgTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGGTGGAAAAAAATTGTTTGACTTTAAAAAAAAAAAAATTTACAGAAAAAAAAAAAAAAAAACCAACGGGGGCCGGCTCTTTTAGACGCCAAAATaaaa                                                       >  1:666271/1‑150 (MQ=255)
                                                                                     aaaTGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGTTGCAAATAGATTGCTTGACTTAACAAACAGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTAAATTAGAAGCTGGc                                                 <  1:478184/151‑1 (MQ=255)
                                                                                     aaaTGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGTTGCAAATAGATTGCTTGACTTAACAAACAGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTAAATTAGAAGCTGGc                                                 <  1:334216/151‑1 (MQ=255)
                                                                                       aTGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGTTGCAAATAAATTTTTTGACTTAAAAAACAAATAAATTGTCAGAAAAAATAAAAAAAAAAACAGCGGGCGCTGGCTCTTTTAGAAGCTAAATTAAAAAATGGCg                                                >  1:536447/1‑150 (MQ=255)
                                                                                               aTGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGGTGTAAAAAAATTGCTTTGATTAAAAAAAAAATAAATTGAAAAAAAAAAAAAAAAAAAAAACAACGGGGGCCGGCTCTTTCAAACACCAAAATAAAAAATAGCGTTACGCgg                                        >  2:350590/1‑150 (MQ=255)
                                                                                                 gTAATATTCCGTAACAGGATGATCGTTATGGCGGGGGGTGAAAAAGATTGCTTTAATTTACAAAAAGATAAATTTAAAGAAAAAATAAAAAAAAAAACAGCGGGGGCTGGGTTTTTAAAACGCCAAATTAAAAAATTGCGGTTCGCGGAg                                      >  1:405885/1‑150 (MQ=255)
                                                                                                     tatTCCGTAACAGGATGATCGTTATGGCGGGGTGGGGAAGACATTTCTTTATTTGACAAAAACAGAAATTGTCAGAAAAAAAAAAAAAAGAACGAACGGGCGCCGGGCCTTGGAGACACTTAATTAGAAGCTGGCggttccccgagt                                     >  1:755499/1‑136 (MQ=255)
                                                                                                         ccGTAACAGGATGATCGTTATGGCGGGGGGGCAAATATAATGCTTGAATTAAAAAAAAAATAAATTTACAGAAAAAATAAAAAAAAAAACAGCGGGCGCTGGCTCTTGAAGAAGCTAAAATAAAAAAAGGGGGTACGCGGAGGAAGTggg                              >  1:593697/1‑150 (MQ=255)
                                                                                                          cGTAACAGGATGATCGTTATGGCGGGGGTGGAAAAAGAATGCTTTACTTTAAAAAAAGAAAAATTTACAGAAAAGAAAAAAAAAAAACCAGCCGGCGCTGGCTCTTTAAGACGCTAAAATAAAAAATGGCGTTACGCGGAGTACGgggg                              >  1:760140/1‑149 (MQ=255)
                                                                                                                      atCGTTATGGCGGGGTTGCAAATAGATTGCTTGACTTAACAAACAGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTAAATTAGAAGCTGGCGTTACGCGGAGTACGTGGGAACGGAatcacatc                <  2:336025/151‑1 (MQ=255)
                                                                                                                                    gTTGCAAATAGATTGCTTGACTTAACAAACAGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTAAATTAGAAGCTGGCGTTACGCGGAGTACGTGGGAACGGAATCACATCACGTACGTTTTGCa  <  2:302841/151‑1 (MQ=255)
                                                                                                                                     |                                                                                                                                                     
GAATGCCAAAAAATAGTATGAAAATTGTGCTATTAGCTAAGAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGTTGCAAATAGATTGCTTGACTTAACAAACAGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTAAATTAGAAGCTGGCGTTACGCGGAGTACGTGGGAACGGAATCACATCACGTACGTTTTGCA  >  NC_000913/987361‑987643

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑