Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,228,2750TC43.5% 44.1 / 12.1 48pseudogene (335/1287 nt)mdtQpseudogene; putative channel/filament proteins
Reads supporting (aligned to +/- strand):  ref base T (14/12);  new base C (8/12);  total (23/25)
Fisher's exact test for biased strand distribution p-value = 3.88e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTTTCTATTTGCTGCAAGACCGTGTTTAACGCCGCCTGGGTTTGCCACTCCCAGTACAGGCGGGCTACGCTGCCAGCCAGCAATTGGCGG‑GTTTGCTCGCGTTCC‑GCCGCCCGTGCTTTAACC‑GTACCCAGGCGGGCAGT‑AACCTCCGCCCGATTCTTTCCCCAGATATCGAGATGCCA‑GCCCGCCGTTAAGCCAAAAGTACCGTTGGTGTACCACGGGCCGGTCGTACCTGCGGCCGGATCGTTCAGAGCAAACGGCCCCATTAAGCCTTCTGCCGACATTTTTTGC  >  NC_000913/2228131‑2228418
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ttttCTATTTGCTGCAAGACCGTGTTTAACGCCGCCTGGGTTTGCCACTCCCAGTACAGGCGGGCTACGCTGCCAGCCAGCAATTGGCGG‑GGTTGCTCGCGTTCC‑GCCCCCCGGGCTTTAAAC‑GTACCCCAGCGGGGAGT‑AAACTCCGccc                                                                                                                                            >  1:610420/1‑151 (MQ=255)
  ttCTATTTGCTGCAAGACCGTGTTTAACGCCGCCTGGGTTTGCCACTCCCAGTACAGGCGGGCTACGCTGCCAGCCAGCAATTGGCGG‑GGTTGATCGGGGTGC‑GGCGCCCCGTCTTTTAAC‑GCAACCCGGAGGGGAGT‑GACCGcccccc                                                                                                                                            >  2:61177/1‑149 (MQ=255)
    cTATTTGCTGCAAGACCGTGTTTAACGCCGCCTGGGTTTGCCACTCCCAGTACAGGCGGGCTACGCTGCCAGCCCGCAATTGGCGG‑GGTTTCCCGCCTTTC‑GCCCCCCGTGCTTTAACC‑CTACCCAGGCGGGGAGT‑AACCTCCGCCCGCtt                                                                                                                                        >  1:510833/1‑151 (MQ=255)
       tttGCTGCAAGACCGTGTTTAACGCCGCCTGGGTTTGCCACTCCCAGTACAGGCGGGCTACGCTGCCAGCCAGCAATTGGCGG‑GGTTTCTCGCGTTCC‑GCCGCCCCTGCTTTAACC‑GTAACCAGGCGGGGAGG‑AACCCCCGCCCGGTtttt                                                                                                                                     >  1:505244/1‑151 (MQ=255)
        ttGCTGCAAGACCGTGTTTAACGCCGCCTGGGTTTGCCACTCCCAGTACAGGCGGGCTACGCTGCCAGCCAGCAATTGGCGG‑GTTTGCTCGCGTTCC‑GCCGCCCGTGCTTTAACC‑GTACCCAGGCGGGCAGT‑AACCTCCGCCCGATTCtt                                                                                                                                     <  1:105393/150‑1 (MQ=255)
         tgctgcAAGACCGTGTTTAACGCCGCCTGGGTTTGCCACTCCCAGTACAGGCGGGCTACGCTGCCAGCCAGCAATTGGCGG‑GTTTGCTCGCGTTCC‑GCCGCCCGTGCTTTAACC‑GTACCCAGGCGGGCAGT‑AACCTCCGCCCGATTCttt                                                                                                                                    <  2:511920/150‑1 (MQ=255)
          gctgcAAGACCGTGTTTAACGCCGCCTGGGTTTGCCACTCCCAGTACAGGCGGGCTACGCTGCCAGCCAGCAATTGGCGG‑GTTTGCTCGCGTTCC‑GCCGCCCGTGCTTTAACC‑GTACCCAGGCGGGCAGT‑AACCTCCGCCCGATTCTTTcc                                                                                                                                  <  2:508215/151‑1 (MQ=255)
               aaGACCGTGTTTAACGCCGCCTGGGTTTGCCACTCCCAGTACAGGCGGGCTACGCTGCCAGCCAGCAATTGGCGG‑GGTTGCTCGCGGTTC‑GCCCCCCCTGCTTTTACC‑GTAACCAGGCGGGGAGT‑AACCCCCGCCCCGTTCTTTtccc                                                                                                                                >  1:78304/1‑148 (MQ=255)
                 gACCGTGTTTAACGCCGCCTGGGTTTGCCACTCCCAGTACAGGCGGGCTACGCTGCCAGCCAGCAATTGGCGG‑GTTTGGTCGCGTTCC‑GCCCCCCCCGCCTTAACC‑CTACCCCGGCGGGCAGG‑AACCTCCGCCCGCTTTTTTtcccc                                                                                                                               >  2:367903/1‑146 (MQ=255)
                 gACCGTGTTTAACGCCGCCTGGGTTTGCCACTCCCAGTACAGGCGGGCTACGCTGCCAGCCAGCAATTGGCGG‑GGTTGCTCGCGTTTC‑CCCCCCCCTGCTTTTACC‑CTACCCAGGCGGGCAGT‑AACCTCCCCCCGGTTCTTTtccc                                                                                                                                >  1:740244/1‑146 (MQ=255)
                  aCCGTGTTTAACGCCGCCTGGGTTTGCCACTCCCAGTACAGGCGGGCTACGCTGCCAGCCAGCAATTGGCGG‑GTTTGCTCGCGTTCC‑GCCGCCCGTGCTTTAACC‑GTACCCAGGCGGGCAGT‑AACCTCCGCCCGATTCTTTCCCCAGatat                                                                                                                          <  1:239937/151‑1 (MQ=255)
                  aCCGTGTTTAACGCCGCCTGGGTTTGCCACTCCCAGTACAGGCGGGCTACGCTGCCAGCCAGCAATTGGCGG‑GGTTTCTCGCGTTCC‑GCCCCCCCTGCTTTAAAC‑GTACCCCGGCGGGCAGT‑AACCTCCCCCCGAATCTTTTCCCAGata                                                                                                                           >  1:392682/1‑150 (MQ=255)
                   ccGTGTTTAACGCCGCCTGGGTTTGCCACTCCCAGTACAGGCGGGCTACGCTGCCAGCCAGCAATTGGCGG‑GTTTGCTCGCGTTCC‑GCCGCCCGTGCTTTAACC‑GTACCCAGGCGGGCAGT‑AACCTCCGCCCGATTCTTTCCCCAGATATc                                                                                                                         <  1:306822/151‑1 (MQ=255)
                       gtTTAACGCCGCCTGGGTTTGCCACTCCCAGTACAGGCGGGCTACGCTGCCAGCCAGCAATTGGCGG‑GTTTTCTCGCGTTTC‑GCCGCCCCGGCCTTTACC‑CTACCCCGGCGGGCAGG‑AAACTCCCCCCGAGCCTTTCCCCCGATATCg                                                                                                                        >  2:191074/1‑148 (MQ=255)
                       gtTTAACGCCGCCTGGGTTTGCCACTCCCAGTACAGGCGGGCTACGCTGCCAGCCAGCAATTGGCGG‑GTTTGCTCGCGTTCC‑GCCGCCCGTGCTTTAACC‑GTACCCAGGCGGGCAGT‑AACCTCCGCCCGATTCTTTCCCCAGATATCgag                                                                                                                      <  1:113018/150‑1 (MQ=255)
                        tttAACGCCGCCTGGGTTTGCCACTCCCAGTACAGGCGGGCTACGCTGCCAGCCCGCAATTGGCGG‑GTTTGCTCCCGCTCC‑CCCGCCCGTGCTTTTAAC‑CCACCCAAGGGGGGAGG‑AAACCCCGccccggtttttttcc                                                                                                                                >  1:781595/1‑127 (MQ=255)
                         ttAACGCCGCCTGGGTTTGCCACTCCCAGTACAGGCGGGCTACGCTGCCAGCCAGCAATTGGCGG‑GTTTGCTCGCGTTCC‑GCCGCCCGTGCTTTAACC‑GTACCCAGGCGGGCAGT‑AACCTCCGCCCGATTCTTTCCCCAGATATCGAGAt                                                                                                                    <  2:308181/150‑1 (MQ=255)
                          tAACGCCGCCTGGGTTTGCCACTCCCAGTACAGGCGGGCTACGCTGCCAGCCAGCAATTGGCGG‑GGTTTGTCGCGTTCC‑GCCGCCCGGGCTTTTACC‑CGAACCCGGCGGGCCGG‑AAACCCCCCCCCCTTCTTTTCCCCGataacc                                                                                                                        >  2:757010/1‑142 (MQ=255)
                               ccgccTGGGTTTGCCACTCCCAGTACAGGCGGGCTACGCTGCCAGCCAGCAATTGGCGG‑GTTTGCTCGCGTTCC‑GCCGCCCGTGCTTTAACC‑GTACCCAGGCGGGCAGT‑AACCTCCGCCCGATTCTTTCCCCAGATATCGAGATGCCA‑Gcc                                                                                                            <  1:314612/151‑1 (MQ=255)
                                 gccTGGGTTTGCCACTCCCAGTACAGGCGGGCCACGCTGCCAGCCAGCAATTGGCGG‑GGTTGGCCGCGGTCC‑CCCCCCCCGGCCTTAACC‑CCACCCCGGCGGGCAGG‑AACCCCCCCCCCATTCTTTCCCCAGGTAATGAGATGGCA‑Gccc                                                                                                           >  2:12997/1‑150 (MQ=255)
                                    tGGGTTTGCCCCTCCCAGTACAGGCGGGCTACGCTGCCAGCCAGCACTTGGCCG‑GTTTTCTCTCGTTCC‑CCCCCCCCTGCTTTTACC‑CGTCCCCGGCGGGCCCG‑GACCCCCCCCCCGTTCTTTTCCCCGCTATTCCGATGCCC‑Gcccccc                                                                                                        >  2:85613/1‑150 (MQ=255)
                                    tGGGTTTGCCACTCCCAGTACAGGCGGGCTACGCTGCCAGCCAGCAATTGGCGG‑GGTTTCTCTCGGTCCACCCCCCCGGGTTTTAACA‑TTCCCCA‑GCGGGCAGTCAACCCCCCCCCG‑TTTTTTCCCCCCGTATTGAGGTGGCc‑gcccgcc                                                                                                        >  2:280180/1‑150 (MQ=255)
                                     ggttttGCCCCTCCCAGTACAGCGGGGCTCCGCGTCCCGCCAGCAATTGGGGG‑TTTTACTCGCTTTCC‑GCCGCCCGGGTTTTAACC‑TTACCCAGGGGGGCAGT‑ACCCTCCGCCCGATTCTTTCCCCATATTTGGAGATGCCA‑GCCCGCCGt                                                                                                      <  2:861051/148‑1 (MQ=255)
                                            ccccccccAGTGGAGGCGGCCTCCGCGGCCAGCCCGCAAGGGGCGT‑GTTTGCTCGCGTTCC‑GCCGCCCGTGTTTTACCC‑TTCCCCAGGCGGGCAGT‑ACCCCCCTCCCGATTCTTCCCCCAGTTATCGAAATCCCA‑CCCCGCCGTTAAGCCa                                                                                               <  2:589895/146‑1 (MQ=255)
                                             cACTCCCAGTACAGGCGGGCTACGCTGCCAGCCAGCAATTGGCGG‑GTTTTCTCCCGTTCC‑CCCGCCCGTGCTTTTAAC‑GGACCCCGGGGGGCAGTAAACCCCCCCCCCATTTTTTCCCC‑CATATCGAGATGCCA‑GCCCCCCCTTAAGcc                                                                                                >  2:313302/1‑149 (MQ=255)
                                              aCTCCCAGTACAGGCGGGCTACGCTGCCAGCCAGCAATTGGCGG‑GGTTGCTCGCGTTCC‑GCCGCCCCGGCTTTAACC‑CGACCCACGCGGGCCGT‑AAACTCCGCCCGATTTTTTCCCCAGATATCGAGATGCCA‑GCCCGCCCTTAAGCCaa                                                                                              >  1:151342/1‑150 (MQ=255)
                                                    aGTACAGGCGGGCTACGCTGCCAGCCAGCAATTGGCGG‑TTTTGCTCGCGTTCC‑GCCGCCCGTGCTTTACCC‑GTACCCAGGCGGGCAGT‑ACCCTCCGCCCGATTCTTTCCCCAGATATCGAGATGCCA‑GCCCGCCGTTAAGCCAAAAGTAc                                                                                        <  1:137943/150‑1 (MQ=255)
                                                      tACGGGCGGGCTCCGCTGCCAGCCAGCAATTGGCGG‑TTTTGCTCGCGTTCC‑GCCGCCCGTGTTTTAACC‑GTCCCAGGGGGGGCAGT‑AACCCCCCCCCGATTCTTTCCCCAGATATCGAGATGCCA‑GCCCGCCGTTAAGCCAAAAGTACCg                                                                                      <  1:413812/150‑1 (MQ=255)
                                                                   cGCTGCCAGCCAGCAATTGGCGG‑GTTTGCTCGCGTTCC‑GCCGCCCGTGCTTTAACC‑GTACCCAGGCGGGCAGT‑AACCTCCGCCCGATTCTTTCCCCAGATATCGAGATGCCA‑GCCCGCCGTTAAGCCCAAAGTACCGTTGGTGTACCAccg                                                                        >  2:23253/1‑149 (MQ=255)
                                                                   cGCTGCCAGCCAGCAATGGGCGG‑GTTTGCCCGCGTCCC‑GCCCCCCTTGTTTTACCC‑GACCCCAGGCGGTAAGC‑ACCCCCCCCCCTATTTTTCCCCCAGATATCGAGATGCCA‑CCCCGCCGTTAAGCCAAAAGTACCGTTGGTGTACCACgg                                                                        <  2:246271/151‑1 (MQ=255)
                                                                    gCTGCGAGCCA‑CAGTTGGGGGTGTTCGTTCGCGTTCC‑G‑CGTCCGTTCTTTTACCGGTCCCCGGGGGGGCTGT‑ACCCCCCCCCCGATTTTTTCCCCAGATGCCCAGTGGCCG‑GCCCGCCGTTAAGCCAAAAGTACCGTTGGTGTACCACggg                                                                       <  2:457501/151‑1 (MQ=255)
                                                                    gCTGCCAGCCAGCAATTGGCGG‑GTTTGCTCGCGTTCC‑GCCGCCCGTGCTTTAACC‑GTACCCAGGCGGGCAGT‑AACCTCCGCCCGATTCTTTCCCCAGATATCGAGATGCCA‑GCCCGCCGTTAAGCCAAAAGTACCGTTGGGGTACCACggg                                                                       >  1:734596/1‑151 (MQ=255)
                                                                       gccagccaGCAATTGGCGG‑GTTTGCTCGCGTTCC‑GCCGCCCGTGCTTTAACC‑GTACCCAGGCGGGCAGT‑AACCTCCGCCCGATTCTTTCCCCAGATATCGAGATGCCA‑GCCCGCCGTTAAGCCAAAAGTACCGTTGGTGTACCACGGGcc                                                                     >  1:458269/1‑150 (MQ=255)
                                                                        ccagccagAAATGGGCGG‑GTTTGCTCGCGTCCC‑GCCGCCCGTGCTTTACCC‑GTCCCCAGGCGGGCAGT‑ACCCCCCGCCCGATTCTTCCCCCAGATATCGAGATGCCA‑GCCCGCCGTTAAGCCAAAAGTACCGTTGGTGTACCACGGGc                                                                      <  1:677703/148‑1 (MQ=255)
                                                                         cagccagcAATTGGCGG‑GTTTGCTCGTGTTCC‑GCCCCCCGTGTTTTAACC‑GTTCCCGGGCGGGAAGT‑ACCCCCCGCCCGTTTTTTTCCCCAGATAGCGAGGTCCCA‑GCCCGCCGTTAAGCCAAAAGTACCGTTGGTGTACCACGGGcc                                                                     <  1:839710/148‑1 (MQ=255)
                                                                             cagcAATTGGCGG‑GTTTGCTCGCGTTCC‑GCCGCCCGTGTTTTAACC‑GTCCCCAGGCGGGCAGT‑AACCTCCGCCCGATTCTTCCCCCAGATATCGAGATGCCA‑GCCCGCCGTTAAGCCAAAAGTACCGTTGGTGTACCACGGGCCGGTCg                                                                <  1:124745/149‑1 (MQ=255)
                                                                                                       tCC‑GCCGCCCGTGCTTTAACC‑GTACCCAGGCGGGCAGT‑AACCTCCGCCCGATTCTTTCCCCAGATATCGAGATGCCA‑GCCCGCCGTTAAGCCAAAAGTACCGTTGGTGTACCACGGGCCGGTCGTACCTGCGGCCGGATCGTTCAGAGCa                                      >  2:205548/1‑150 (MQ=255)
                                                                                                        cc‑gccgCCCGTGTTTTACCC‑GTCCCCAGGCGGGCGTT‑ACCCCCCCCCCATTTCTTCCCCCAGATATCGAGATGCCG‑GCCCGCCGTTAAGCCAAAAGTACCGTTGGTGTACCACGGGCCGGTCGTACCTGCGGCCGGATCGTTCAGAGCaaa                                    <  2:106226/151‑1 (MQ=255)
                                                                                                        cc‑gccgCCCGTGCTTTACCC‑GTCCCCAGGCGGGCAGT‑ACCCCCCGCCCGATTCTTCCCCCAGATATCGAGATGCCA‑GCCCGCCGTTAAGCCAAAAGTACCGTTGGTGTACCACGGGCCGGTCGTACCTGCGGCCGGATCGTTCAGAGc                                       <  1:757202/148‑1 (MQ=255)
                                                                                                         c‑gccgcCCGTGCTTTAACC‑GTACCCAGGCGGGCAGT‑AACCTCCGCCCGATTCTTTCCCCAGATATCGAGATGCCA‑GCCCGCCGTTAAGCCAAAAGTACCGTTGGTGTACCACGGGCCGGTCGTACCTGCGGCCGGATCGTTCAGAGCAAAc                                   >  2:48882/1‑151 (MQ=255)
                                                                                                             cgccCGTGCTTTAACC‑GTACCCAGGCGGGCAGT‑AACCTCCGCCCGATTCTTTCCCCAGATATCGAGATGCCA‑GCCCGCCGTTAAGCCAAAAGTACCGTTGGTGTACCACGGGCCGGTCGTACCTGCGGCCGGATCGTTCAGAGCAAACGGc                                >  1:693829/1‑151 (MQ=255)
                                                                                                               cccGTGCTTTAACC‑GTCCCCAGGCGGGCAGT‑ACCCCCCGCCCGATTCTTTCCCCAGATATCGAGATGCCA‑GCCCGCCGTTAAGCCAAAAGTACCGTTGGTGTACCACGGGCCGGTCGTACCTGCGGCCGGATCGTTCAGAGCAAACGGccc                              <  1:811675/151‑1 (MQ=255)
                                                                                                                ccGTGCTTTACCC‑TTCCCCGGGGGGGAAGA‑ACCCCCCGCCCGATTCTTCCCCCAGATATCGAGATGCCC‑GCCCGCCGTTAAGCCAAAAGTACCGTTGGTGTACCACGGGCCGGTCGTACCTGCGGCCGGATCGTTCAGAGCAAACGGcccc                             <  1:397221/151‑1 (MQ=255)
                                                                                                                      tttAGCC‑GTCCCCGGGCGGGAAGT‑AACCGCCGCCCGATTCTTTCCCCAGATAGCGAGATGCCA‑GCCCGCCGTTAAGCCAAAAGTACCGTTGGTGTACCACGGGCCGGTCGTACCTGCGGCCGGATCGTTCAGAGCAAACGGCCCCAtt                          <  2:814321/148‑1 (MQ=255)
                                                                                                                        tAACC‑GTACCCAGGCGGGGAGT‑ACCCCCCGCCCGATTCTTTCCCCAGATATGGAAATCCCA‑GCCCGCCGTTAAGCCAAAAGTACCGTTGGTGTACCACGGGCCGGTCGTACCTGCGGCCGGATCGTTCAGAGCAAACGGCCCCATTAAGc                      <  1:428167/150‑1 (MQ=255)
                                                                                                                            cgcaccccGGGCGGACAAA‑AACCTCCCCCCGATTCTTCCCCGAGATATCGCGA‑GCCAGGCCCGCCGTTAAGCCAAAAGTACCGTTGGTGTACCACGGGCCGGTCGTACCTGCGGCCGGATCGTTCAGAGCAAACGGCCCCa                            <  2:632978/136‑1 (MQ=255)
                                                                                                                                       cGGGCAGT‑AACCTCCGCCCGATTCTTTCCCCAGATATCGAGATGCCA‑GCCCGCCGTTAAGCCAAAAGTACCGTTGGTGTACCACGGGCCGGTCGTACCTGCGGCCGGATCGTTCAGAGCAAACGGCCCCATTAAGCCTTCTGCCGACAttt       >  1:759821/1‑151 (MQ=255)
                                                                                                                                            aGT‑ACCCCCCGCCCGATTCTTCCCCCAGATATCGAGATGCCA‑GCCCGCCGTTAAGCCAAAAGTACCGTTGGTGTACCACGGGCCGGTCGTACCTGCGGCCGGATCGTTCAGAGCAAACGGCCCCATTAAGCCTTCTGCCGACATTTTTTGc  <  1:581537/151‑1 (MQ=255)
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TTTTCTATTTGCTGCAAGACCGTGTTTAACGCCGCCTGGGTTTGCCACTCCCAGTACAGGCGGGCTACGCTGCCAGCCAGCAATTGGCGG‑GTTTGCTCGCGTTCC‑GCCGCCCGTGCTTTAACC‑GTACCCAGGCGGGCAGT‑AACCTCCGCCCGATTCTTTCCCCAGATATCGAGATGCCA‑GCCCGCCGTTAAGCCAAAAGTACCGTTGGTGTACCACGGGCCGGTCGTACCTGCGGCCGGATCGTTCAGAGCAAACGGCCCCATTAAGCCTTCTGCCGACATTTTTTGC  >  NC_000913/2228131‑2228418

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑