Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*KT24401,288,0590CA22.0% 106.9 / 10.7 50intergenic (+22/+48)slyB/nhaA_1Outer membrane lipoprotein SlyB/Na( )/H( ) antiporter NhaA
Reads supporting (aligned to +/- strand):  ref base C (17/22);  new base A (11/0);  total (28/22)
Fisher's exact test for biased strand distribution p-value = 1.08e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

GATGGCAGCATGCGCGCCTATGTGCAGGCCGTGCAGGAGAACGAAATCTTCCGTGTTGGCGACCGAGTGCGCATCATGACTGTAGACGGTACCAGTCGCGTTTCGCACTGACCGTAGTGCAGTAATAAAAAACCCCGACATGGCTGC‑TGCCAGTCGGGGTTTTTTCATGCCTCAGCCAAGTCAGGCAATGCTGGTTTTGCGGCTGGCCATTGCGGTGACGGCGTAGCCGATCACCGCAGCAAAGAACGAACCAGTAAGAATGCCCATGC  >  KT2440/1287927‑1288195
                                                                                                                                    |                                                                                                                                         
gatgGCAGCATGCGCGCCTATGTGCAGGCCGTGCAGGAGAACGAAATCTTCCGTGTTGGCGACCGAGTGCGCATCATGACTGTAGACGGTACCAGTCGCGTTTCGCACTGACCGTAGTGCAGTAATAAAAAACCCCg                                                                                                                                       <  3:92856/137‑1 (MQ=255)
gatgGCAGCATGCGCGCCTATGTGCAGGCCGTGCAGGAGAACGAAATCTTCCGTGTTGGCGACCGAGTGCGCATCATGACTGTAGACGGTACCAGTCGCGTTTCGCACTGACCGTAGTGCAGTAATAAAAAACCCCg                                                                                                                                       <  1:4134/137‑1 (MQ=255)
             gcgcCTATGTGCAGGCCGTGCAGGAGAACGAAATCTTCCGTGTTGGCGACCGAGTGCGCATCATGACTGTAGACGGTACCAGTCGCGTTTCGCACTGACCGTAGTGCAGTAATAAAAAACCCCCACATtgctgc‑tgc                                                                                                                         >  5:297819/1‑137 (MQ=255)
               gcCTATGTGCAGGCCGTGCAGGAGAACGAAATCTTCCGTGTTGGCGACCGAGTGCGCATCATGACTGTAGACGGTACCAGTCGCGTTTCGCACTGACCGTAGTGCAGTAATAAAAAACCCCGACATGGCTGC‑TGCCa                                                                                                                       <  1:99916/137‑1 (MQ=255)
                ccTATGTGCAGGCCGTGCAGGAGAACGAAATCTTCCGTGTTGGCGACCGAGTGCGCATCATGACTGTAGACGGAACCAGTCGCGTTTCGCACTGACCGTAGTGCAGAAAAAAAAAACCCCGACATGGCTGC‑TGCCAg                                                                                                                      <  1:301440/137‑1 (MQ=255)
                    tgtgCAGGCCGTGCAGGAGAACGAAATCTTCCGCGTTGGCGACCGCGTGCGCATCATGCCTGTCGACGGTACAAGTCGCTTTGCGCACTGACCGTAGTGCAGTAATAAAAAACCCCGACATGGCTGC‑TGCCAGTCgg                                                                                                                  <  7:298476/137‑1 (MQ=255)
                       gCAGGCCGTGCAGGAGAACGAAATCTTCCGTGTTGGCGACCGAGTGCGCATCATGACTGTAGACGGTACCAGTCGCGTTTCGAACTGACCGTAGTGCAGTAATAAAAAACCCCGACAAGGCTGC‑TGGCAAGCGGGGt                                                                                                               >  6:282210/1‑137 (MQ=255)
                           gCCGTGCAGGAGAACGAAATCTTCCGTGTTGGCGACCGAGTGCGCATCATGACTGTAGACGGTACCAGTCGCGTTTCGCACTGACCGTAGGGCAGTAATAAAAAACCCCGACATGGCTGC‑TGCCAGTCGGGGttttt                                                                                                           <  1:230292/137‑1 (MQ=255)
                           gCCGTGCAGGAGAACGAAATCTTCCGTGTTGGCGACCGAGTGCGCATCATGACTGTAGACGGTACCAGTCGCGTTTAGCACTGACCGTAGTGCAGTAATAAAAAAACCCGACATTGCTGC‑TGCCAGTCGGGGttttt                                                                                                           >  7:257878/1‑137 (MQ=255)
                           gCCGTGCAGGAGAACGAAATCTTCCGTGTTGGCGACCGAGTGCACATCATGACTGTAGACGGTACCAGTCGCGTTTCGCACTGACCGTAGTGCAGTAATAAAAAACCCCGACATGGCTGC‑TGCCAGTCGGGGttttt                                                                                                           <  3:40082/137‑1 (MQ=255)
                              gTGCAGGAGAACGAAATCTTCCGTGTTGGCGACCGAGTGCGCATCATGACTGTAGACGGTACCAGTCGCGTTTCGCACTGACCGTAGTGCAGTAATAAAAAAccc                                                                                                                                         <  8:220268/105‑1 (MQ=255)
                              gTGCAGGAGAACGAAATCTTCCGTGTTGGCGACCGAGTGCGCATCATGACTGTAGACGGTACCAGTCGCGTTTCGCACTGACCGTAGTGCAGTAATAAAAAAccc                                                                                                                                         >  7:220268/1‑105 (MQ=255)
                              gTGCAGGAGAACGAAATCTTCCGTGTTGGCGACCGAGAGCGCATCATGACTGTAGACGGTACCAGACGCGTTTAGCACACACACTACTGCATTAAAAAAAAAACACGACATGGCTGC‑TTCCAGTCGGGGttttttgt                                                                                                        >  7:160744/1‑135 (MQ=255)
                                gCAGGAGAACGAAATCTTCCGTGTTGGCGACCGAGTGCGCATCATGACTGTAGACGGTACCAGTCGCGGTTGGGCCTGGGCGTTGTGGAGTTATAAAAAAAAACGACAAGGGGGG‑GGGCAGTGGGGGtgtttttttt                                                                                                      >  1:342045/1‑133 (MQ=255)
                                 cAGGAGAACGAAATCTTCCGTGTTGGCGACCGAGTGCGCATCATGACTGTAGACGGTACCAGTCGCGTTTCGCACTGCCCGTAGTGGAGTAATAAAAAACCCCCACATGGCTGC‑TGCCAGTCGGGGTTTTTTAAttc                                                                                                     >  3:339029/1‑135 (MQ=255)
                                  aGGAGAACGAAATCTTCCGTGTTGGCGACCGAGTGCGCATCATGACTGTAGACGGTACCAGTCGCGTTTCGCACTGACCGTAGTGCAGTAATAAAAAACCCCGACATGGCTGC‑TGCCAGTCGGGGTTTTTTCATGcc                                                                                                    >  8:68166/1‑137 (MQ=255)
                                  aGGAGAACGAAATCTTCCGTGTTGGCGACCGAGTGCGCATCATGACTGTAGACGGTACCAGTCGCGTTTCGCACTGACCGTAGTGCAGTAATAAAAAACCCCGACATGGCTGC‑TGCCAGTCGGGGTTTTTTCATGcc                                                                                                    >  7:51178/1‑137 (MQ=255)
                                   ggAGAACGAAATCTTCCGTGTTGGCGACCGAGTGCGCATCATGACTGTAGACGGTACCAGTCGCGTTTCGCACTGGCCGTTGTGCAGTAATTAAAAACACCGACCAGGGTGCTTGCCGGCGGGGGTTTTTACagccg                                                                                                    >  7:118719/1‑133 (MQ=255)
                                    gagaACGAAATCTTCCGTGTTGGCGACCGAGTGCGCATCATGACTGTAGACGGTACCAGTCGCGTTTCGCACTGACCGTAGTGCAGTAATAAAAAACCCCGACATGGCTGC‑TGCCAGTCGGGGTTTTTTCATGCCTc                                                                                                  <  7:4447/137‑1 (MQ=255)
                                        aCGAAATCTTCCGTGTTGGCGACCGAGTGCGCATCATGACTGTAGACGGTACCAGTCGCGTTTAGCACTGAACGTAGTGCAGTAATAAAAAACACCCACAATGCGGG‑TTCCAGTCGGGGGTTTTTAATTCCTCAGcc                                                                                              >  4:264707/1‑137 (MQ=255)
                                         cGAAATCTTCCGTGTTGGCGACCGAGTGCGCATCATGACTGTAGACGGTACCAGTCGCGTTTAGCACGGACCCTAGTGCAGTAATAAAAAAACCCCACAAGGCGGC‑TGCCAGTCGGGGTTTTTTGATTGCTCAGCCa                                                                                             >  2:230292/1‑137 (MQ=255)
                                                             aCCGAGTGCGCATCATGACTGTAGACGGTACCAGTCGCGTTTATCACTGTCCGGAGTTCAGTAATAAAAAAAACCCACATGGCTGC‑TGGCACTAGGGGTTTTTTAATGGCAAAGGCAAGTGAGGCAATTGGGGtttt                                                                         >  5:324075/1‑137 (MQ=255)
                                                                gAGTGCGCATCATGACTGTAGACGGTACCAGTCGCGTTTCGCACTGACCGTAGTGCAGTAATAAAAAACCCCGACATGGCTGC‑TGCCAGTCGGGGTTTTTTCATGCCTCAGCCAAGTCAGGCAATGCTGGTTTTGCg                                                                      <  2:342045/137‑1 (MQ=255)
                                                                              aCTGTAGACGGTACCAGTCGCGTTTCGCACTGACCGTAGTGCAGTAATAAAAAACCCCGACATGGCTGC‑TGCCAGTCGGGGTTTTTTCATGCCTCAGCCAAGTCAGGCAATGCTGGTTTTGCGGCTGGCCATTGCgg                                                        <  5:37633/137‑1 (MQ=255)
                                                                               cTGTAGACGGTACCAGTCGCGTTTCGCACTGACCGTAGTGCAGTAATAAAAAACCCCGACATGGCTGC‑TGCCAGTCGGGGTTTTTTCATGCCTCAGCCAAGTCAGGCAATGCTGGTTTTGCGGCTGGCCATTGCGGt                                                       >  4:277237/1‑137 (MQ=255)
                                                                                  acagcGGTACCAGTCGCGTTTCGCACTGACCGTAGTGCAGTAATAAAAAACCCCGACATGGCTGC‑TGCCAGTCGGGGTTTTTTCATGCCTCAGCCAAGTCAGGCAATGCTGGTTTTGCGGCTGGCCATTGCGGTGAc                                                    <  7:22490/133‑1 (MQ=255)
                                                                                   aGACGGTACCAGTCGCGTTTCGCACTGACCGTAGTGCAGTAATAAAAAACCCCGACATGGCTGC‑TGCCAGTCGGGGTTTTTTCATGCCTCAGCCAAGTCAGGCAATGCTGGTTTTGCGGCTGGCCATTGCGGTGACg                                                   <  7:298102/137‑1 (MQ=255)
                                                                                          aCCAGTCGCGTTTAGCACTGACCGTTGTGCAGTAATAAAAAAAACCCACATGGCTGC‑TGACAGTCGGTGTTTTTTGATGGCTCAACAGAGTCAGGCAATGCTGGTTTTGCTGCTGGCCAATGCGGTGAAgggctagg                                            >  8:24471/1‑131 (MQ=255)
                                                                                          aCCAGTCGCGTTTAGCACTGACCGTAGTGCAGTAATAAAAAAACCCCCCAAGGCTGG‑TGGCAGTAGGGGGTTTTTAAAGCCTCAGCCAAATCATGCAATTCAGGTTTTGGGGCTGGCCATTGCGGTGACGGCGTAGc                                            >  8:98931/1‑137 (MQ=255)
                                                                                           ccAGTCGCGTTTCGCACTGACCGTAGTGCAGTAATAAAAAACCCCGACATGGCTGC‑TGCCAGTCGGGGTTTTTTCATGCCTCAGCCAAGTCAGGCAATGCTGGTTTTGCGGCTGGCCATTGCGGTGACGGCGTAGcc                                           <  5:184276/137‑1 (MQ=255)
                                                                                            cAGTCGCGTTTCGAACTGAACCTTGTGCAGTAATAAAAAAACCCCACAAGGCTGC‑TGCCAGTCGGGGTTTTTTAATTCCACAACCAAATCACTCAAAGCTGGTTTTTAGGCTGGCCATTTAGGTTACGGCGTATccc                                          >  2:239235/1‑136 (MQ=255)
                                                                                             aGTCGCGTTTCGCACTGACCGTTGTGCAGTAATAAAAAAACCCGACATGGCTGC‑TGCCAGTCGGGGGTTTTTGATGCCTCAGGCCAGGAAGGCAATGCGGGGTTTTCGGGTGGCCATTGCGGTGACGGCGGAGCCgg                                         >  2:16157/1‑136 (MQ=255)
                                                                                                 gcgTTTGGCACTGCCCGGAGTGCAGTAATAAAAAAACCCCCCATGGCGGC‑GGCCAGTCGGGGGTTTTTAAAGCCTCAGCCAAGTCAGGCAATTCTGGTTTTGGGGGTGGCCATTTCGGTGCCCGCGTTGCCGATAAc                                     >  6:27781/1‑137 (MQ=255)
                                                                                                 gcgTTTCGCCCAGACCGTAGTGGAGTAATAAAAAACCCCGACAAGGGGGC‑TGCCAGTCGGGGGTTTTTGAAGCCTCAGCCAAATCAGGCAATGGGGGTTTTTCGGCGGGCCAATTCGGTGACCGCGTTGCCCCTCAc                                     >  8:58319/1‑137 (MQ=255)
                                                                                                    tttAGCACTGACCGTAGTGCAGTAATAAAAAAACCCCACATGGCTGC‑TGCCAGGCGGGGTTTTTTAATGCCTCAGCCAAGTAAGGCAAAGGTGGTTTTTCGGCTGGCCATTGCGGTGACGGCGTATCCGATcccggt                                  >  8:22490/1‑132 (MQ=255)
                                                                                                            tGACCGTATTTCAGTAATAAAAAACCCCGACATGGCTGC‑TGCCAGTCGGGGTTTTTTCATGCCTCAGCCAAGTCAGGCAATGCTGGTTTTGCGGCTGGCCATTGCGGTGACGGCGTAGCCGATCACCGCAGCAAAga                          <  2:128748/137‑1 (MQ=255)
                                                                                                                cGTAGTGCAGTAATAAAAAACCCCGACATGGCTGC‑TGCCAGTCGGGGTTTTTTCATGCCTCAGCCAAGTCAGGCAATGCTGGTTTTGCGGCTGGCCATTGCGGTGACGGCGTAGCCGATCACCGCAGCAAAgaacga                      >  6:119991/1‑137 (MQ=255)
                                                                                                                 gTAGTGCAGTAATAAAAAACCCCGACATGGCTGC‑TGCCAGTCGGGGTTTTTTCAt                                                                                                       >  3:122440/1‑55 (MQ=255)
                                                                                                                 gTAGTGCAGTAATAAAAAACCCCGACATGGCTGC‑TGCCAGTCGGGGTTTTTTCAt                                                                                                       <  4:122440/55‑1 (MQ=255)
                                                                                                                      gCAGTAATAAAAAACCCCGACATGGCTGC‑TGCCAGTCGGGGTTTTTTCATGCCTCAGCCAAGTCAGGCAATGCTGGTTTTGCGGCTGGCCATTGCGGTGACGGCGTAGCCGATCACCGCAGCAAAGAACGAACCAGt                >  3:298689/1‑137 (MQ=255)
                                                                                                                       cAGTAATAAAAAACCCCGACATGGCTGC‑TGCCAGTCGGGGTTTTTTCATGCCTCAGCCAAGTCAGGCAATGCTGGTTTTGCGGCTGGCCATTGCGGTGACGGCGTAGCCGATCACCGCAGCAAAGAACGAACCAGTa               <  4:63928/137‑1 (MQ=255)
                                                                                                                        aGTAATAAAAAACCCCGACATGGCTGC‑TGCCAGTCGGGGTTTTTTCATGCCTCAGCCAAGTCAGGCAATGCTGGTTTTGCGGCTGGCCATTGCGGTGACGGCGTAGCCGATCACCGCAGCAAAGAACGAACCAGTaa              <  2:337273/137‑1 (MQ=255)
                                                                                                                           aataaAAAACCCCGACATGGCTGC‑TGCCAGTCGGGGTTTTTTCATGCCTCAGCCAAGTCAGGCAATGGTGGTTTTGCGGCTGGCCATTTCGGTGACGGCGTAGCCGATCCCCGCAGCAAAGAACGAACCACgaagaa           >  4:28559/1‑137 (MQ=255)
                                                                                                                           aataaAAAACCCCGACATGGCTGC‑TGCCAGTCGGGGTTTTTTCATGCCTCAGCCAAGTCAGGCAATGCTGGTTTTGCGGCTGGCCATTGCGGTGACGGCGTAGCCGATCACCGCAGCAAAGCACGAACCAGTAAGaa           >  5:51928/1‑137 (MQ=255)
                                                                                                                           aataaAAAACCCCGACATGGCTGC‑TGCCAGTCGGGGTTTTTTCATGCCTCAGCCAAGTCAGGCAATGCTGGTTTTGCGGCTGGCCATTGCGGTGACGGCGTAGCCGATCACCGCAGCAAAGAACGAACCAGTAAGaa           <  8:257878/137‑1 (MQ=255)
                                                                                                                             taaAAAACCCCGACATGGCTGC‑TGCCAGTCGGGGTTTTTTCATGCCTCAGCCAAGTCAGGCAATGCTGGTTTTGCGGCTGGCCATTGCGGTGACg                                                   <  5:235392/95‑1 (MQ=255)
                                                                                                                             taaAAAACCCCGACATGGCTGC‑TGCCAGTCGGGGTTTTTTCATGCCTCAGCCAAGTCAGGCAATGCTGGTTTTGCGGCTGGCCATTGCGGTGACg                                                   >  6:235392/1‑95 (MQ=255)
                                                                                                                                aaaaCCCCGACATGGCTGC‑TGCCAGTCGGGGTTTTTTCATGCCTCAGCCAAGTCAGGCAATGCTGGTTTTGCGGCTGGCCATTGCGGTGACGGCGTAGCCGATCACCGCAGCAAAGAACGAACCAGTAAGAATGccc      <  4:339029/137‑1 (MQ=255)
                                                                                                                                aaaaCCCCGACATGGCTGC‑TGCCAGTCGGGGTTTTTTCATGCCTCAGCCAAGTCAGGCAATGCTGGTTTTGCGGCTGGCCATTGCGGTGACGGCGTAGCCGATCACCGCAGCAAAGAACGAACCAGTAAGAATGccc      <  7:60790/137‑1 (MQ=255)
                                                                                                                                aaaaCCCCGACATGGCTGC‑TGCCAGTCGGGGTTTTTTCATGCCTCAGCCAAGTCAGGCAATGCTGGTTTTGCGGCTGGCCATTGCGGTGACGGCGTAGCCGATCACCGCAGCAAAGAACGAACCAGTAAGAATGccc      <  2:465/137‑1 (MQ=255)
                                                                                                                                aaaaCCCCGACATGGCTGC‑TGCCAGTCGGGGTTTTTTCATGCCTCAGCCAAGTCAGGCAATGCTGGTTTTGCGGCTGGCCATTGCGGTGACGGCGTAGCCGATCACCGCAGCAAAGAACGAACCAGTAAGAATGccc      >  2:243879/1‑137 (MQ=255)
                                                                                                                                  aaCCCCGACATGGCTGC‑TGCCAGTCGGGGTGTTTTCATGCCTCAGCCAAGTCAGGCAATGCTGGTTTTGCGGCTGGCCATTGCGGTGACGGCGTAGCCGATCACCGCAGCAAAGAACTACCCAGTAAGAATGcccct    >  8:64559/1‑135 (MQ=255)
                                                                                                                                    ccccGACATGGCTGC‑TGCCAGTCGGGGTTTTTTCATGCCTCAGCCAAGTCAGGCAATGCTGGTTTTGCGGCTGGCCATTGCGGTGACGGCGTAGCCGATCACCGCAGCAAAGAACGAACCAGTAAGAATGCCCATGc  <  7:68166/137‑1 (MQ=255)
                                                                                                                                    |                                                                                                                                         
GATGGCAGCATGCGCGCCTATGTGCAGGCCGTGCAGGAGAACGAAATCTTCCGTGTTGGCGACCGAGTGCGCATCATGACTGTAGACGGTACCAGTCGCGTTTCGCACTGACCGTAGTGCAGTAATAAAAAACCCCGACATGGCTGC‑TGCCAGTCGGGGTTTTTTCATGCCTCAGCCAAGTCAGGCAATGCTGGTTTTGCGGCTGGCCATTGCGGTGACGGCGTAGCCGATCACCGCAGCAAAGAACGAACCAGTAAGAATGCCCATGC  >  KT2440/1287927‑1288195

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑