Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,056,1150AC66.7% 7.2 / 31.9 36G75G (GGT→GGG) glnLsensory histidine kinase in two‑component regulatory system with GlnG
Reads supporting (aligned to +/- strand):  ref base A (8/4);  new base C (0/24);  total (8/28)
Fisher's exact test for biased strand distribution p-value = 1.64e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.49e-05

AGCTGTTCCTGACTTAAGCGGCGCTGGTTATCCATCGGAGCCATCTCCAGCAGGATCATGCCGTCCGGCATACGCTGGGCCGTCACAGAAAGGATATGCGAGCGCCCGTCGATGACCAGCGTCACTTCGTTATCGGTAAAACCTTGCCCCGCCTCCAGACTTTCTTGCATCAGCTCGATATTTAATGAGAAGTAGCTCAACAGTTCCGGTAACGGTGTACCAAACAATTTGCGGGAGCTTTGGGCGAGCAGTTGTTGCGCGGCAGGGTTGGCGTAATGGATCGCCA  >  NC_000913/4055975‑4056260
                                                                                                                                            |                                                                                                                                                 
aGCTGTTCCTGACTTAAGCGGCGCTGGTTATCCATCGGAGCCATCTCCAGCAGGATCATGCCGTCCGGCATACGCTGGGCCGTCACAGAAAGGATATGCGAGCGCCCGTCGATGACCAGCGTCACTTCGTTATCGGTAAAACCTTGcccc                                                                                                                                          <  1:433767/150‑1 (MQ=255)
            cTTAGGCGGCGCTGTTTATCCACCGGAGCCATCTCAAGCAGGATCAGGCCGTCCGGCATCCGCGGGCCCGACACAGAAAGGATATGCGAGCCCCCGTCGATGACCAGCGTCACTTCTTTATCGGTAAAACCTTGCCCCGCCTCCAGACtt                                                                                                                              <  1:659866/150‑1 (MQ=255)
            cTTAAGCGGCGCTGGTTATCCATCGGAGCCATCTCCAGCAGGATCATGCCGTCCGGCATACGCTGGGCCGTCACAGAAAGGATATGCGAGCGCCCGTCGATGACCAGCGTCACTTCGTTATCGGTAAAACCTTGCCCCGCCTCCAGACttt                                                                                                                             >  1:378032/1‑151 (MQ=255)
               aaGCGGCGCTGGTTATCCATCGGAGCCACCTCCAGCAGGATCATGCCGCCCGGCATACGCGGGGCCGTCAAAGAAAGGATATGCGAGCGCCCGTCGATGACCAGCGTCACTTCGTTATCGGTAAACCCTTGCCCCGCCTCCAGACTTTCtt                                                                                                                          <  1:617509/151‑1 (MQ=255)
                   ggcgCTGTTTACCCATCGGACCCATCTCCAGAAGGATCAGGCCGTCCGGCATCCGCTGGGCCGTCACAGAAAGGATATGCGAGCGCCCGTCGATGACCAGCTTCACTTCGTTATCGGTAAACCCTTGCCCCGCCTCCAGACTTTCTTGCa                                                                                                                       <  1:449188/150‑1 (MQ=255)
                       cTGGTTATCCATCGGAGCCATCTCCAGCAGGATCATGCCGCCCGGAATACGCTGGGCCGTCACAGAAAGGATATGCGAGCGCCCGTCGATGACCGGCGTCACTTCTTTATCGGAAAACCCTTCCCCCGCCTCCAGACTTTCTTGCATCa                                                                                                                    <  1:75473/149‑1 (MQ=255)
                        tGGTTATCCATCGGAGCCATCTCCAGCAGGATCATGCCGTCCGGCATACGCTGGGCCGTCACAGAAAGGATATGCGAGCGCCCGTCGATGACCAGCGTCACTTCGTTATCGGTAAAACCTTGCCCCGCCTCCAGACTTTCTTGCATCAGc                                                                                                                  >  2:423167/1‑150 (MQ=255)
                        tGGTTATCCATCGGAGCCATCTCCAGCAGGATCATGCCGTCCGGCATACGCTGGGCCGTCACAGAAAGGATATGCGAGCGCCCGTCGATGACCAGCGTCACTTCGTTATCGGTAAAACCTTGCCCCGCCTCCAGACTTTCTTGCATCAGCt                                                                                                                 >  2:486689/1‑151 (MQ=255)
                         gtttacccacgggACCCATCCCCGGCAGGTTCATCCCGCCCGGCATACGCTGGGCCGTCACAAAAAGGATATGCGAGCCCCCGTCGATGACCAGCGTCACTTCGTTATCGGTAAACCCTTGCCCCGCCTCCAGACTTTCTTGCATCa                                                                                                                    <  1:16635/136‑1 (MQ=255)
                               ccgtCGGAGCCACCCCCAGAAGGTCCATCCCGTCCGGCATCCGCTGGGCCGCCCAAGAAAGGATAGGCGGGCGCCCGTGGATGACCAGCTCCCCTTCGTTATCGGTAAACCCTTGCCCCGCCTCCAGACTTTCTTGCATCAGCTCGATAtt                                                                                                          <  2:228695/148‑1 (MQ=255)
                                cATCGGAGCCATCTCCAGCAGGATCATGCCGTCCGGCATACGCTGGGCCGTCACAGAAAGGATATGCGAGCGCCCGTCGATGACCAGCGTCACTTCGTTATCGGTAAAACCTTGCCCCGCCTCCAGACTTTCTTGCATCAGCTCGATAtt                                                                                                          >  2:601156/1‑150 (MQ=255)
                                               cagcagGATCATGCCGTCCGGCATACGCTGGGCCGTCACAGAAAGGATATGCGAGCGCCCGTCGATGACCAGCGTCACTTCGTTATCGGTAAAACCTTGCCCCGCCTCCAGACTTTCTTGCATCAGCTCGATATTTAATGAGAAGTAGCTc                                                                                          >  2:461561/1‑151 (MQ=255)
                                                   agGATCATGCCGCCCGGCATCCGCGGGGCCGTCACAGAAAGGATATGCGAGCGCCCGTCGATGCCCAGCGTCATTTCGTTATCGGTAAAACCTTGCCCCGCCTCCAGACTTTCTTGCATCAGCTCGATATTTAATGAGAAGTAGCTc                                                                                          <  1:672533/147‑1 (MQ=255)
                                                   agGATCATGCCGCCCGGCATACGCGGGCCCGTCACAGAAAGGATATGCGAGCCCCCGTCGATGACCAGCTTCACTTCGTTATCGGTAAACCCTTGCCCCGCCTCCAGACTTTCTTGCATCAGCTCGATATTTAATGAGAAGTAGCTCa                                                                                         <  1:670379/148‑1 (MQ=255)
                                                    ggATCATCCCGTCCGGCATACGCTGGGCCGTCACAGAAAGGATATGCGAGCGCCCGTCGATGACCAGCGTCTCTTCGTTATCGGAAAACCCTTGCCCCGCCTCCAGACTTTCTTGCATCAGCTCGATATTTAATGAGAAGTAGCTCaa                                                                                        <  1:257196/148‑1 (MQ=255)
                                                            ccGTCCGGCATCCGCGGGGCCGTCAAAGAAAGGATATGCGGGCCCCCGCCGATGACCAGCTTCACTTCGTTATGGGTAAACCCTGGCCCCGCCTCCAGACTTTCTTGCATCAGCTCGATATTTAATGAGAAGTAGCTCAACAGTTCCg                                                                                <  1:281244/148‑1 (MQ=255)
                                                                ccGGCATACGCTGGGCCGTCACAGAAAGGATATGCGAGCGCCCGTCGATGACCAGCGTCACTTCGTTATCGGTAAACCCTTGCCCCGCCTCCAGACTTTCTTGCATCAGCTCGATATTTAATGAGAAGTAGCTCAACAGTTCCGGTAACg                                                                          <  2:553022/150‑1 (MQ=255)
                                                                ccGGCATACGCGGGGCCGTCACAGAAAGGATATGCGAGCGCCCGTGGATGACCGGCGTCACTTCGTTATCGGTAAACCCTTGCCCCGCCTCCAGACTTTCTTGCATCAGCTCGATATTTAATGAGAAGTAGCTCAACAGTTCCGGTAACgg                                                                         <  2:345622/151‑1 (MQ=255)
                                                                            gggCCGTCACAGAAAGGATATGCGGGCCCCCGTCGATCACCAGCGTCCCTTCGTTATCGGTAAACCCTTGCCCCGCCTCCAGACTTTCTTGCATCAGCTCGATATTTAATGAGAAGTAGCTCAACAGTTCCGGTAACGGTGTACCAAAc                                                               <  1:607543/149‑1 (MQ=255)
                                                                              gCCGTCACAGAAAGGATATGCGAGCGCTCGTCGATGACCAGCGTCACTTCGTTATCGGTAAAACCTTGCCCCGCCTCCAGACTTTCTTGCATCAGCTCGATATTTAATGAGAAGTAGCTCAACAGTTCCGGTAACGGTGTACCAAACAAtt                                                           >  2:722240/1‑151 (MQ=255)
                                                                                     caaaaaGGAAATGCGCGCCCCCGTCGACGACCGCCGCCACTCTTTTACGGGTAAACCCTTCCCCCGCCTCCAGACTTTCTTGCATCAGCTCGATATTTAATGAGAAGTAGCTCAACAGTTCCGGTAACGGTGTACCAAACAATTTGc                                                        <  1:149293/144‑1 (MQ=255)
                                                                                         aaGGATATGCGAGCGCCCGTCGATGACCAGCGTCACTTCGTTATCGGTAAACCCTTCCCCCGCCTCCAGACTTTCTTGCATCAGCTCGATATTTAATGAGAAGTAGCTCAACAGTTCCGGTAACGGTGTACCAAACAATTTGCGGGAGCtt                                                <  1:727693/151‑1 (MQ=255)
                                                                                           gtatatGCGAGCGCCCGTCGATGACCAGCGCCACTTCGTTAGCGTTAAACCCGTGCCCCGCCTCCAGACTTTCTTGCATCAGCTCGATATTTAATGAGAAGTAGCTCAACAGTTCCGGTAACGGTGTACCAAACAATTTGCGGGAGCttt                                               <  1:99871/148‑1 (MQ=255)
                                                                                               atGCGAGCGCCCGTCGATGACCAGCGTCACTTCGTTATCGGTAAACCCTTGCCCCGCCTCCAGACTTTCTTGCATCAGCTCGATATTTAATGAGAAGTAGCTCAACAGTTCCGGTAACGGTGTACCAAACAATTTGCGGGAGCTTTGGGCg                                          <  2:706199/151‑1 (MQ=255)
                                                                                                     gcgcCCGTCGATGACCAGCGTCACTTCGTTATCGGTAAACCCTTGCCCCGCCTCCAGACTTTCTTGCATCAGCTCGATATTTAATGAGAAGTAGCTCAACAGTTCCGGTAACGGTGTACCAAACAATTTGCGGGAGCTTTGGGCGAGCAg                                     <  2:804786/150‑1 (MQ=255)
                                                                                                      cccccGTCGATGACCAGCTTCATTTCGTTATCGGTAAACCCTTGCCCCGCCTCCAGACTTTCTTGCATCAGCTCGATATTTAATGAGAAGTAGCTCAACAGTTCCGGTAACGGTGTACCAAACAATTTGCGGGAGCTTTGGGCGAGc                                       <  2:80484/145‑1 (MQ=255)
                                                                                                         ccGTCGAGGCCCGGCGCCTCTTCTTTATGGATAAAACCTGGCCCCGCCTCCAGACTTTCTTGCATCAGCTCGATATTTAATGAGAAGTAGCTCAACAGTTCCGGTAACGGTGTACCAAACAATTTGCGGGAGCTTTGGGCGAGCAgttgtt                                <  2:258673/151‑1 (MQ=255)
                                                                                                            tCGATAACCGGCGTCACTTCGTTATCGGAAAACCCTTGCCCCGCCTCCAGACTTTCTTGCATCAGCTCGATATTTAATGAGAAGTAGCTCAACAGTTCCGGTAACGGTGTACCAAACAATTTGCGGGAGCTTTGGGCGAGCAGTTGTTgc                              <  1:362104/150‑1 (MQ=255)
                                                                                                                   ccAGCGTCACTTCTTTACCGGTAAACCCTTGCCCCGCCTCCAGACTTTCTTGCATCAGCTCGATATTTAATGAGAAGTAGCTCAACAGTTCCGGTAACGGTGTACCAAACAATTTGCGGGAGCTTTGGGCGAGCAGTTGTTGCGCGGc                         <  2:443748/148‑1 (MQ=255)
                                                                                                                   ccAGCGTCACTTCGTTATCGGTAAACCCTTGCCCCGCCTCCAGACTTTCTTGCATCAGCTCGATATTTAATGAGAAGTAGCTCAACAGTTCCGGTAACGGTGTACCAAACAATTTGCGGGAGCTTTGGGCGAGCAGTTGTTGCGCGGCAg                       <  2:259398/150‑1 (MQ=255)
                                                                                                                       cGTCACTTCGTTATCGGTAAAACCTTGCCCCGCCTCCAGACTTTCTTGCATCAGCTCGATATTTAATGAGAAGTAGCTCAACAGTTCCGGTAACGGTGTACCAAACAATTTGCGGGAGCTTTGGGCGAGCAGTTGTTGCGCGGCAGGGTTg                  >  1:493915/1‑151 (MQ=255)
                                                                                                                        gTCCCTTCGTTATCGGTAAACCCTTGCCCCGCCTCCAGACTTTCTTGCATCAGCTCGATATTTAATGAGAAGTAGCTCAACAGTTCCGGTAACGGTGTACCAAACAATTTGCGGGAGCTTTGGGCGAGCAGTTGTTGCGCGGCAGGGTTg                  <  2:834635/150‑1 (MQ=255)
                                                                                                                             ttgtttACCGTTAAACCCTTCCCCCGCCTCCAGACTTTCTTGCATCAGCTCGATATTTAATGAGAAGTAGCTCAACAGTTCCGGTAACGGTGTACCAAACAATTTGCGGGAGCTTTGGGCGAGCAGTTGTTGCGCGGCAGGGtt                   <  1:68483/140‑1 (MQ=255)
                                                                                                                                 ttATCGGTAAAACCTTGCCCCGCCTCCAGACTTTCTTGCATCAGCTCGATATTTAATGAGAAGTAGCTCAACAGTTCCGGTAACGGTGTACCAAACAATTTGCGGGAGCTTTGGGCGAGCAGTTGTTGCGCGGCAGGGTTGGCGTAATgg         >  1:510226/1‑150 (MQ=255)
                                                                                                                                 ttATCGGAAAACCCTTGCCCCGCCTCCAGACTTTCTTGCATCAGCTCGATATTTAATGAGAAGTAGCTCAACAGTTCCGGTAACGGTGTACCAAACAATTTGCGGGAGCTTTGGGCGAGCAGTTGTTGCGCGGCAGGGTTGGCGTAATg          <  2:558116/149‑1 (MQ=255)
                                                                                                                                     cGGTAAACCCTTCCCCCGCCTCCAGACTTTCTTGCATCAGCTCGATATTTAATGAGAAGTAGCTCAACAGTTCCGGTAACGGTGTACCAAACAATTTGCGGGAGCTTTGGGCGAGCAGTTGTTGCGCGGCAGGGTTGGCGTAATGGATCg     <  1:397977/150‑1 (MQ=255)
                                                                                                                                         aacaCCTTCCTCCGCCTCCAGACTTTCTTGCATCAGCTCGATATTGAATGAGAAGTAGCTCAACAGTTCCGGTAACGGTGTACCAAACAATTTGCGGGAGGTTTGGGCGAGCAGTTGTTGCGCGGCAGGGTTGGCGTAATGGa        <  1:66759/140‑1 (MQ=255)
                                                                                                                                         aaacCCTTGCCCCGCCTCCAGACTTTCTTGCATCAGCTCGATATTTAATGAGAAGTAGCTCAACAGTTCCGGTAACGGTGTACCAAACAATTTGCGGGAGCTTTGGGCGAGCAGTTGTTGCGCGGCAGGGTTGGCGTAATGGATCGCCa  <  2:810737/149‑1 (MQ=255)
                                                                                                                                            |                                                                                                                                                 
AGCTGTTCCTGACTTAAGCGGCGCTGGTTATCCATCGGAGCCATCTCCAGCAGGATCATGCCGTCCGGCATACGCTGGGCCGTCACAGAAAGGATATGCGAGCGCCCGTCGATGACCAGCGTCACTTCGTTATCGGTAAAACCTTGCCCCGCCTCCAGACTTTCTTGCATCAGCTCGATATTTAATGAGAAGTAGCTCAACAGTTCCGGTAACGGTGTACCAAACAATTTGCGGGAGCTTTGGGCGAGCAGTTGTTGCGCGGCAGGGTTGGCGTAATGGATCGCCA  >  NC_000913/4055975‑4056260

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑