Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,056,1150AC49.0% 50.5 / 15.9 49G75G (GGT→GGG) glnLsensory histidine kinase in two‑component regulatory system with GlnG
Reads supporting (aligned to +/- strand):  ref base A (17/8);  new base C (0/24);  total (17/32)
Fisher's exact test for biased strand distribution p-value = 2.20e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCTGTAGCTGTTCCTGACTTAAGCGGCGCTGGTTATCCATCGGAGCCATCTCCAGCAGGATCATGCCGTCCGGCATACGCTGGGCCGTCACAGAAAGGATATGCGAGCGCCCGTCGATGACCAGCGTCACTTCGTTATCGGTAAAA‑CCTTGCCCCGCCTCCAGACTTTCTTGCATCAGCTCGATATTTAATGAGAAGTAGCTCAACAGTTCCGGTAACGGTGTACCAAACAATTTGCGGGAGCTTTGGGCGAGCAGTTGTTGCGCGGCAGGGTTGGCGTAATGGATCGC  >  NC_000913/4055970‑4056258
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gCTGTAGCTGTTCCTGACTTAAGCGGCGCTGGTTATCCATCGGAGCCATCTCCAGCAGGATCATGCCGTCCGGCATACGCTGGGCCGTCACAGAAAGGATATGCGAGCGCCCGTCGATGACCAGCGTCACTTCGTTATCGGTAAAA‑CCtt                                                                                                                                             <  1:54954/150‑1 (MQ=255)
gCTGTAGCTGTTCCTGACTTAAGCGGCGCTGGTTATCCATCGGAGCCATCTCCAGCAGGATCATGCCGTCCGGCATACGCTGGGCCGTCACAGAAAGGATATGCGAGCGCCCGTCGATGACCAGCGTCACTTCGTTATCGGTAAAA‑CCTTg                                                                                                                                            >  2:693953/1‑151 (MQ=255)
   gTAGCTGTTCCTGACTTAAGCGGCGCTGGTTATCCATCGGAGCCATCTCCAGCAGGATCATGCCGTCCGGCATACGCTGGGCCGTCACAGAAAGGATATGCGAGCGCCCGTCGATGACCAGCGTCACTTCGTTATCGGTAAAA‑CCTTGccc                                                                                                                                         >  1:394534/1‑151 (MQ=255)
    tAGCTGTTCCTGACTTAAGCGGCGCTGGTTATCCATCGGAGCCATCTCCAGCAGGATCATGCCGTCCGGCATACGCTGGGCCGTCACAGAAAGGATATGCGAGCGCCCGTCGATGACCAGCGTCACTTCGTTATCGGTAAAA‑CCTTGcccc                                                                                                                                        >  1:980179/1‑151 (MQ=255)
         gTTCCTGACTTAAGCGGCGCTGGTTATCCATCGGAGCCATCTCCAGCAGGATCATGCCGTCCGGCATACGCTGGGCCGTCACAGAAAGGATATGCGAGCGCCCGTCGATGACCAGCGTCACTTCGTTATCGGTAAAA‑CCTTGCCCCGCCTc                                                                                                                                   >  2:616379/1‑151 (MQ=255)
                  ttAAGCGGCGCGGTTTATCCAGCGGACCCATCTCCAGCGGGATCAGGCCGCCCGGCATACGCTGGGCCGTCACAAAAAGGATATGCGAGCGCCCGTCGATGACCAGCGTCACTTCGTTATCGGTAAAC‑CCTTGCCCCGCCTCCAGACtt                                                                                                                            <  1:144182/149‑1 (MQ=255)
                      gcggcgCTGGTTATCCATCGGAGCCATCTCCAGCAGGATCATGCCGTCCGGCATACGCTGGGCCGTCACAGAAAGGATATGCGAGCGCCCGTCGATGACCAGCGTCACTTCGTTATCGGTAAAA‑CCTTGCCCCGCCTCCAGACTTTCTTGc                                                                                                                      >  2:784497/1‑151 (MQ=255)
                        ggcgCTGGTTATCCATCGGAGCCATCTCCAGCAGGATCATGCCGTCCGGCATCCGCTGGGCCGTCACAAAAAGGATATGCGAGCGCCCGTCGATGACCAGCGTCACTTCGTTATCGGTAAAA‑CCTTGCCCCGCCTCCAGACTTTCTTGCa                                                                                                                     <  2:980270/150‑1 (MQ=255)
                               gTTATCCATCGGAGCCATCTCCAGCAGGATCATGCCGTCCGGCATACGCTGGGCCGTCACAGAAAGGATAGGCGGGCGCCCGTCGATGACCAGCGTCACTTCGTTATCGGTAAAC‑CCTTGCCCCGCCTCCAGACTTTCTTGCATCAg                                                                                                                 <  1:550029/147‑1 (MQ=255)
                                ttACCCATCGGAGCCATCTCCAGCAGGATCATGCCGCCCGGCATACGCTGGGCCGTCACAGAAAGGATATGCGAGCGCCCGTCGATGACCAGCTTCACTTCGTTATCGGAAAAC‑CCTTGCCCCGCCTCCAGACTTTCTTGCATCAGCTCg                                                                                                             <  2:675154/150‑1 (MQ=255)
                                    ccATGGGAGCCATCTCCAGCAGGATCATGCCGCCCGGCATACGCTGGGCCGTCACAGAAAGGATATGCGAGCGCCCGTCGATGCCCAGCGTCACTTCGTTATCGGTAAAC‑CCTTGCCCCGCCTCCAGACTTTCTTGCATCAGCTCGATAtt                                                                                                        <  2:520562/151‑1 (MQ=255)
                                         ggAGCCATCTCCAGCAGGATCATGCCGTCCGGCATACGCTGGGCCGTCACAGAAAGGATATGCGAGCGCCCGTCGATGACCAGCGTCACTTCGTTATCGGTAAAA‑CCTTGCCCCGCCTCCAGACTTTCTTGCATCAGCTCGATATTTAATg                                                                                                   >  1:20/1‑151 (MQ=255)
                                             ccATCCCCAGCAGGATCATCCCGTCCGGCATGCGCTGGGCGGTCACAGAAAGTATAGGCGAGCGCCCGTCGATGACCAGCGCCTCTTCGTTGTCGGTAAAC‑CCTTCCCCCGCCTCCAGACTTTCTTGCATCAGCTCGATATTTAATGAGaa                                                                                               <  2:409626/151‑1 (MQ=255)
                                                                gCCGTCCGGCATACGCTGGGCCGTCACAGAAAGGATATGCGAGCGCCCGTCGATGACCAGCGTCACTTCGTTATCGGTAAAA‑CCTTGCCCCGCCTCCAGACTTTCTTGCATCAGCTCGATATTTAATGAGAAGTAGCTCAACAGTTCCGGt                                                                            >  1:997771/1‑151 (MQ=255)
                                                                 cggcccGGCATCCGCGGGGCCTTAACAGAAAGGATATGCGACCGCCCGCCGATACCCAGCGCCACTTCTTTACCGGTAAAC‑CCTTGCCCCGCCTCCAGACTTTCTTGCATCAGCTCGATATTTAATGAGAAGTAGCTCAACAGTTcc                                                                               <  1:229314/143‑1 (MQ=255)
                                                                 ccGTCCGGCATCCGCTGGGCCGTCACAAAAAGAATATGCGAGCGCCCGTCGATGCCCAGCTTCATTTCGTTATCGGTAAAC‑CCTTGCCCCGCCTCCAGACTTTCTTGCATCAGCTCGATATTTAATGAGAAGTAGCTCAACAGTTCCGGt                                                                            <  1:961775/150‑1 (MQ=255)
                                                                 ccGTCCGGCATACGCTGGGCCGTCACAGAAAGGATATGCGAGCCCCCGTCGATGCCCAGCGTCACTTCTTTATCGGTAAAC‑CCTTGCCCCGCCTCCAGACTTTCTTGCATCAGCTCGATATTTAATGAGAAGTAGCTCAACAGTTCCGGTa                                                                           <  2:426943/151‑1 (MQ=255)
                                                                     ccGGCATACGCTGGGCCGTCACAGAAAGGATATGCGAGCGCCCGTCGATGCCCAGCGTCACTTCTTTATCGGTAAAA‑CCTTGCCCCGCCTCCAGACTTTCTTGCATCAGCTCGATATTTAATGAGAAGTAGCTCAACAGTTCCGGTAACgg                                                                       <  1:606702/151‑1 (MQ=255)
                                                                     ccGGCATACGCTGGGCCGTCACAGAAAGGATATGCGACCCCCCGTCGATGACCAGCGTCACTTCTTTATCGGTAAAC‑CCTTCCCCCGCCTCCAGACTTTCTTGCATCAGCTCGATATTTAATGAGAAGTAGCTCAACAGTTCCGGTAACg                                                                        <  1:688654/150‑1 (MQ=255)
                                                                         cATACGCGGGGCCGTCACAGAAAGGATAGGCGAGCGCCCGTCGATGACCAGCGTCACTTCTTTATCGGTAAAA‑CCTTGCCCCGCCTCCAGACTTTCTTGCATCAGCTCGATATTTAATGAGAAGTAGCTCAACAGTTCCGGTAACGGTGTa                                                                   <  1:868611/151‑1 (MQ=255)
                                                                            aCGCTGGGCCGTCACAGAAAGGATATGCGAGCGCCCGTCGATGACCAGCGTCACTTCGTTATCGGTAAAA‑CCTTGCCCCGCCTCCAGACTTTCTTGCATCAGCTCGATATTTAATGAGAAGTAGCTCAACAGTTCCGGTAACGGTGTAcc                                                                 >  1:511813/1‑150 (MQ=255)
                                                                            aCGCTGGGCCGTCACAGAAAGGATATGCGAGCGCCCGTCGATGACCAGCGTCACTTCGTTATCGGTAAAA‑CCTTGCCCCGCCTCCAGACTTTCTTGCATCAGCTCGATATTTAATGAGAAGTAGCTCAACAGTTCCGGTAACGGTGTAcc                                                                 >  1:689241/1‑150 (MQ=255)
                                                                             cGCTGGGCCGTCACAGAAAGGATATGCGAGCGCCCGTCGATGACCAGCGTCACTTCGTTATCGGTAAAA‑CCTTGCCCCGCCTCCAGACTTTCTTGCATCAGCTCGATATTTAATGAGAAGTAGCTCAACAGTTCCGGTAACGGTGTACCa                                                                >  1:422253/1‑150 (MQ=255)
                                                                                 gggCCGTCACAGAAAGGATATGCGAGCGCCCGTCGATGACCAGCATCACTTCTTTACCGATAAAC‑CCTTGCCCCGCCTCCAGACTTTCTTGCATCAGCTCGATATTTAATGAGAAGTAGCTCAACAGTTCCGGTAACGGTGTACCAAAc                                                             <  2:889378/149‑1 (MQ=255)
                                                                                 gggCCGTCACAAAAAGGATATGCGAGCCCCCGTCGATGCCCAGCTTCACTTCTTTATCGTTAAAC‑CCTGGCCCCGCCTCCAGACTTTCTTGCATCAGCTCGATATTTAATGAGAAGTAGCTCAACAGTTCCGGTAACGGTGTa                                                                   <  1:868820/143‑1 (MQ=255)
                                                                                     cGTCACAGAAAGGATATGCGAGCGCCCGTCGATGACCAGCGTCACTTCGTTATCGGTAAAA‑CCTTGCCCCGCCTCCAGACTTTCTTGCATCAGCTCGATATTTAATGAGAAGTAGCTCAACAGTTCCGGTAACGGTGTACCAAACAATTTg                                                       >  1:505592/1‑151 (MQ=255)
                                                                                        cacaGAAAGAATATGCGCCCGCCCCTGGATGACCAGCTTCTTTTTTTTATCGGTAAAA‑CCTTCCCCCGCCTCCAGACTTTCTTGCATCAGCTCGATATTTAATGAGAAGTAGCTCAACAGTTCCGGTAACGGTGTACCAAACAATTTGc                                                      <  1:799154/149‑1 (MQ=255)
                                                                                        caaaaaaaGGATATGCGAGCGCCCGTCGATGCCCAGCGTCCCTTCTTTATCGGTAAAA‑CCTTCCCCCGCCTCCAGACTTTCTTGCATCAGCTCGATATTTAATGAGAAGTAGCTCAACAGTTCCGGTAACGGTGTACCAAACAATTTGc                                                      <  2:439689/144‑1 (MQ=255)
                                                                                             aaaGGATATGCGAGCGCCCGTCGATGCCCAGCGTCCCTTCGTTATCGGTAAAC‑CCTGGCCCCGCCTCCAGACTTTCTTGCATCAGCTCGATATTTAATGAGAAGTAGCTCAACAGTTCCGGTAACGGTGTACCAAACAATTTGCGGGAGc                                                <  2:663395/150‑1 (MQ=255)
                                                                                             aaaGGATATGCGAGCGCCCGTCGATGCCCAGCGTCACTTCGTTATCGGTAAAC‑CCTTGCCCCGCCTCCAGACTTTCTTGCATCAGCTCGATATTTAATGAGAAGTAGCTCAACAGTTCCGGTAACGGTGTACCAAACAATTTGCGGGAGCt                                               <  2:297669/151‑1 (MQ=255)
                                                                                                ggATATGCGAGCGCCCGTCGATGACCAGCGTCACTTCGTTATCGGAAAAC‑CCTTGCCCCGCCTCCAGACTTTCTTGCATCAGCTCGATATTTAATGAGAAGTAGCTCAACAGTTCCGGTAACGGTGTACCAAACAATTTGCGGGAGCttt                                             <  2:966931/150‑1 (MQ=255)
                                                                                                 gATATGCGAGCGCCCGTCGATGACCAGCGTCACTTCGTTATCGGTAAAA‑CCTTGCCCCGCCTCCAGACTTTCTTGCATCAGCTCGATATTTAATGAGAAGTAGCTCAACAGTTCCGGTAACGGTGTACCAAACAATTTGCGGGAGCTTTgg                                           >  1:1056585/1‑151 (MQ=255)
                                                                                                      gCGAGCGCCCGCCGATGCCCAGCGTCCTTTCGTTA‑CGGAAAAACCCTGGCCCCGCCTCCAGACTTTCTTGCATCAGCTCGATATTTAATGAGAAGTAGCTCAACAGTTCCGGTAACGGTGTACCAAACAATTTGCGGGAGCTTTGGGc                                         <  2:610178/148‑1 (MQ=255)
                                                                                                          gcccccGTCGATGACCAGCGTCACTTCTTTATCGGTAAAC‑CCTTGCCCCGCCTCCAGACTTTCTTGCATCAGCTCGATATTTAATGAGAAGTAGCTCAACAGTTCCGGTAACGGTGTACCAAACAATTTGCGGGAGCTTTGGGCGAGCAg                                   <  2:731968/147‑1 (MQ=255)
                                                                                                           cgcCCGTCGATGACCAGCGTCATTCCGTTATCGGAAAAC‑CCTTGCCCCGCCTCCAGACTTTCTTGCATCAGCTCGATATTTAATGAGAAGTAGCTCAACAGTTCCGGTAACGGTGTACCAAACAATTTGCGGGAGCTTTGGGCGAGc                                     <  1:262682/147‑1 (MQ=255)
                                                                                                             cccGTCGATGCCCAGCGTCACTTCGTTATCGGTAAAC‑CCTTGCCCCGCCTCCAGACTTTCTTGCATCAGCTCGATATTTAATGAGAAGTAGCTCAACAGTTCCGGTAACGGTGTACCAAACAATTTGCGGGAGCTTTGGGCGAGCAgttgt                               <  2:89843/151‑1 (MQ=255)
                                                                                                                gTCTATGACCAGCGTCACTTCGTTATCGGAAAAC‑CCTTGCCCCGCCTCCAGACTTTCTTGCATCAGCTCGATATTTAATGAGAAGTAGCTCAACAGTTCCGGTAACGGTGTACCAAACAATTTGCGGGAGCTTTGGGCGAGCAgtt                                 <  1:823345/146‑1 (MQ=255)
                                                                                                                    aTGCCCAGTGTCACTCCTTTATCGATAAAA‑CCTTGCCCCGCCTCCAGACTTTCTTGCATCAGCTCGATATTTAATGAGAAGTAGCTCAACAGTTCCGGTAACGGTGTACCAAACAATTTGCGGGAGCTTTGGGCGAGCAGTTGTTGCGCgg                        <  2:693324/151‑1 (MQ=255)
                                                                                                                     tGACCAGCGTCACTTCGTTATCGGTAAAA‑CCTTGCCCCGCCTCCAGACTTTCTTGCATCAGCTCGATATTTAATGAGAAGTAGCTCAACAGTTCCGGTAACGGTGTACCAAACAATTTGCGGGAGCTTTGGGCGAGCAGTTGTTGCGCGGc                       >  2:20528/1‑151 (MQ=255)
                                                                                                                          aGCGTCCCTTCGTTACCGTTAAAC‑CTTTGCCCCGCCTCCAGACTTTCTTGCATCAGCTCGATATTTAATGAGAAGTAGCTCAACAGTTCCGGTAACGGTGTACCAAACAATTTGCGGGAGCTTTGGGCGAGCAGTTGTTGCGCGGCAggg                   <  2:576682/150‑1 (MQ=255)
                                                                                                                            cGTCTCTTCGTTATCGTAAAAC‑CCTTGCCCCGCCTCCAGACTTTCTTGCATCAGCTCGATATTTAATGAGAAGTAGCTCAACAGTTCCGGTAACGGTGTACCAAACAATTTGCGGGAGCTTTGGGCGAGCAGTTGTTGCGCGGCAGGGtt                 <  1:426699/150‑1 (MQ=255)
                                                                                                                            cGTCACTTCGTTATCGGTAAAA‑CCTTGCCCCGCCTCCAGACTTTCTTGCATCAGCTCGATATTTAATGAGAAGTAGCTCAACAGTTCCGGTAACGGTGTACCAAACAATTTGCGGGAGCTTTGGGCGAGCAGTTGTTGCGCGGCAGGGTTg                >  2:615863/1‑151 (MQ=255)
                                                                                                                            cGTCACTTCGTTATCGGTAAAA‑CCTTGCCCCGCCTCCAGACTTTCTTGCATCAGCTCGATATTTAATGAGAAGTAGCTCAACAGTTCCGGTAACGGTGTACCAAACAATTTGCGGGAGCTTTGGGCGAGCAGTTGTTGCGCGGCAGGGTTg                >  1:207815/1‑151 (MQ=255)
                                                                                                                             gTCACTTCGTTATCGGTAAAA‑CCTTGCCCCGCCTCCAGACTTTCTTGCATCAGCTCGATATTTAATGAGAAGTAGCTCAACAGTTCCGGTAACGGTGTACCAAACAATTTGCGGGAGCTTTGGGCGAGCAGTTGTTGCGCGGCAGGGTTgg               >  2:291122/1‑151 (MQ=255)
                                                                                                                                  ttCTTTATCGGTAAAC‑CCTTGCCCCGCCTCCAGACTTTCTTGCATCAGCTCGATATTTAATGAGAAGTAGCTCAACAGTTCCGGTAACGGTGTACCAAACAATTTGCGGGAGCTTTGGGCGAGCAGTTGTTGCGCGGCAGGGTTGGCGt            <  1:694413/149‑1 (MQ=255)
                                                                                                                                        aTCGGTAAAA‑CCTTGCCCCGCCTCCAGACTTTCTTGCATCAGCTCGATATTTAATGAGAAGTAGCTCAACAGTTCCGGTAACGGTGTACCAAACAATTTGCGGGAGCTTTGGGCGAGCAGTTGTTGCGCGGCAGGGTTGGCGTAATGGATc    >  1:427706/1‑151 (MQ=255)
                                                                                                                                        aTCGGAAAAC‑CCTGGCCCCGCCTCCAGACTTTCTTGCATCAGCTCGATATTTAATGAGAAGTAGCTCAACAGTTCCGGTAACGGTGTACCAAACAATTTGCGGGAGCTTTGGGCGAGCAGTTGTTGCGCGGCAGGGTTGGCGTAATGGATc    <  1:452953/151‑1 (MQ=255)
                                                                                                                                         ccGGAAAAC‑CCTTACCCCGCCTCCAGACTTTCTTGCATCAGCTCGATATTTAATGAGAAGTAGCTCAACAGTTCCGGTAACGGTGTACCAAACAATTTGCGGGAGCTTTGGGCGAGCAGTTGTTGCGCGGCAGGGTTGGCGTAATGGAt     <  2:101081/148‑1 (MQ=255)
                                                                                                                                           ggTAAAC‑CCTTGCCCCGCCTCCAGACTTTCTTGCATCAGCTCGATATTTAATGAGAAGTAGCTCAACAGTTCCGGTAACGGTGTACCAAACAATTTGCGGGAGCTTTGGGCGAGCAGTTGTTGCGCGGCAGGGTTGGCGTAATGGATCGc  <  2:394539/150‑1 (MQ=255)
                                                                                                                                                 |                                                                                                                                                
GCTGTAGCTGTTCCTGACTTAAGCGGCGCTGGTTATCCATCGGAGCCATCTCCAGCAGGATCATGCCGTCCGGCATACGCTGGGCCGTCACAGAAAGGATATGCGAGCGCCCGTCGATGACCAGCGTCACTTCGTTATCGGTAAAA‑CCTTGCCCCGCCTCCAGACTTTCTTGCATCAGCTCGATATTTAATGAGAAGTAGCTCAACAGTTCCGGTAACGGTGTACCAAACAATTTGCGGGAGCTTTGGGCGAGCAGTTGTTGCGCGGCAGGGTTGGCGTAATGGATCGC  >  NC_000913/4055970‑4056258

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑