Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,228,2360GC44.4% 29.8 / 10.5 27pseudogene (374/1287 nt)mdtQpseudogene; putative channel/filament proteins
Reads supporting (aligned to +/- strand):  ref base G (5/10);  new base C (9/3);  total (14/13)
Fisher's exact test for biased strand distribution p-value = 5.42e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

CATTTTCCCCGCGACATCGTTGAGCTGCTGCCGGGTTTTGCTGGCATTAATATCGGTTTCCACACCTTCAACTGAAGAAGTAATCCCGTTCTGATATAGCTGGCGATCGGTCGCGATAATGGTGTTCTGCTCTTTTTCTATTTGCTGCAAGACCGTGTTTAACGCCG‑CCTGGGTTTGCCACTCCCAGTACAGGCGGGCTACGCTGCCAGCCAGCAATTGGCGGG‑TTTGCT‑CG‑CG‑TTCCGCCGCCCGTGCTTTAACC‑GTACCCAGGCGGGCAGTAACCTCCGCCCGATTC‑TTTCCCCAGATATCGAGATGCCAGCCCGCC‑GTTAAG‑CCAAAAGTACCGTTGGTGTACCACGGGCCGGTCGTACCTGCGGCCGGATCGTTC‑AGAG‑CA‑AACGGCCCCATTAAGCCTTCTGCCGACATTTTTTGCCGCTCCATATCCGCCGAAAAGTC  >  NC_000913/2227998‑2228441
                                                                                                                                                                                                                                                   |                                                                                                                                                                                                                    
cattttcCCCGCGACATCGTTGAGCTGCTGCCGGGTTTTGCTGGCATTAATATCGGTTTCCACACCTTCAACTGAAGAAGTAATCCCGTTCTGATATAGCTGGCGATCGGTCGCGATAATGGTGTTCTGCTCTTTTTCTATTTGCTGCAAGACCGTGTTTAACGCCG‑CCTGGGTTTGCCACTCCCAGTACAGGCGGGCTACGCTGCCAGCCAGCAATTGGCGGG‑TTTGCT‑CG‑CG‑TTccg                                                                                                                                                                                                                      <  2:350217/239‑1 (MQ=255)
            gACATCGTTGAGCTGCTGCCGGGTTTTGCTGGCATTAATATCGGTTTCCACACCTTCAACTGAAGAAGTAATCCCGTTCTGATATAGCTGGCGATCGGTCGCGATAATGGTGTTCTGCTCTTTTTCTATTTGCTGCAAGACCGTGTTTAACGCCG‑CCTGGGTTTGCCACTCCCAGTACAGGCGGGCTACGCTGCCAGCCAGCAATTGGCGGG‑TTTGCT‑CG‑CG‑TTCCGCCGCCCGTGCtt                                                                                                                                                                                                          <  1:912409/239‑1 (MQ=255)
               aTCGTTGAGCTGCTGCCGGGTTTTGCTGGCATTAATATCGGTTTCCACACCTTCAACTGAAGAAGTAATCCCGTTCTGATATAGCTGGCGATCGGTCGCGATAATGGTGTTCTGCTCTTTTTCTATTTGCTGCAAGACCGTGTTTAACGCCG‑CCTGGGTTTGCCACTCCCAGTTCAGGCGGGCTACGCTGCCAGCCAGCAATTGGCGGG‑TTTGCT‑CG‑CG‑TTCCGCCGCCCGTGCTTTaa                                                                                                                                                                                                       <  2:1397545/239‑1 (MQ=255)
                              ccGGGTTTTGCTGGCATTAATATCGGTTTCCACACCTTCAACTGAAGAAGTAATCCCGTTCTGATATAGCTGGCGATCGGTCGCGATAATGGTGTTCTGCTCTTTTTCTATTTGCTGCAAGACCGTGTTTAACGCCG‑CCTGGGTTTGCCACTCCCAGTACAGGCGGGCTACGCTGCCAGCCAGCAATTGGCGGG‑TTTGCT‑CG‑CG‑TTCCGCCGCCCGTGCtt                                                                                                                                                                                                          <  1:1134606/221‑1 (MQ=255)
                                                       gTTTCCACACCTTCAACTGAAGAAGTAATCCCGTTCTGATATAGCTGGCGATCGGTCGCGATAATGGTGTTCTGCTCTTTTTCTATTTGCTGCAAGACCGTGTTTAACGCCG‑CCTGGGTTTGCCACTCCCAGTACAGGCGGGTTACGCTGCCAGCCAGCAATTGGCGGG‑TTTGCT‑CG‑CG‑TTCCGCCGCCCGTGCTTTAACC‑GTACCCAGGCgg                                                                                                                                                                                        <  1:1383415/213‑1 (MQ=255)
                                                       gTTTCCACACCTTCAACTGAAGAAGTAATCCCGTTCTGATATAGCTGGCGATCGGTCGCGATAATGGTGTTCTGCTCTTTTTCTATTTGCTGCAAGACCGTGTTTAACGCCG‑CCTGGGTTTGCCACTCCCAGTACAGGCGGGCTACGCTGCCAGCCAGCAATTGGCGGG‑GTTGTT‑CC‑CG‑TTCCGCCGCCCCTGCTTTAACC‑GCACCCAGGCGGGCAGTAACCTCCCCCCGAt                                                                                                                                                                     >  1:322774/1‑232 (MQ=255)
                                                           ccACACCTTCAACTGAAGAAGTAATCCCGTTCTGATATAGCTGGCGATCGGTCGCGATAATGGTGTTCTGCTCTTTTTCTATTTGCTGCAAGACCGTGTTTAACGCCG‑CCTGGGTTTGCCACTCCCAGTACAGGCGGGCTACGCTGCCAGCCAGCAATTGGCGGG‑TTTGCT‑CG‑CG‑TTCCGCCGCCCGTGCTTTAACC‑GTACCCAGGCGGGCAGTAACCTCCGCCCGATTC‑TTTCCCCAg                                                                                                                                                         <  2:815292/239‑1 (MQ=255)
                                                                 cTTCAACTGAAGAAGTAATCCCGTTCTGATATAGCTGGCGATCGGTCGCGATAATGGTGTTCTGCTCTTTTGCTATTTGCTGCAAGACCGTGTTTAACGCCG‑CCTGGGTTTGCCACTCCCAGTACAGGCGGGCTACGCTGCCAGCCAGCAATTGGCGGG‑GTTGGT‑CG‑CG‑TTCCCCCGCCCGTGCTTTTACC‑CTATACAGGCGGGCAGTAACACCCCCCCGAGTC‑TTTtccccgcgattc                                                                                                                                                   >  1:1299849/1‑231 (MQ=255)
                                                                        tGAAGAAGTAATCCCGTTCTGATATAGCTGGCGATCGGTCGCGATAATGGTGTTCTGCTCTTTTTCTATTTGCTGCAAGACCGTGTTTAACGCCG‑CCTGGGTTTGCCACTCCCAGTACAGGCGGGCTACGCTGCCAGCCAGCAATTGGCGGG‑TTTGCT‑CG‑CG‑TTCCGCCGCCCGTGCTTTAACC‑GTACCCAGGCGGGCAGTAACCTCCg                                                                                                                                                                           <  1:1347368/209‑1 (MQ=255)
                                                                                  aTCCCGTTCTGATATAGCTGGCGATCGGTCGCGATAATGGTGTTCTGCTCTTTTTCTATTTGCTGCAAGACCGTGTTTAACGCCG‑CCTGGGTTTGCCACTCCCAGTACAGGCGGGCTCCGCTGCCAGCCACCAATTGGCGGG‑TTTGCTCCC‑CG‑TCCCCCCCCCCGGCCTTTAACC‑TACCCCCGGCGGGCGGTAACccccccccccctttt                                                                                                                                                                 >  2:1347368/1‑203 (MQ=255)
                                                                                        ttCTGATATAGCTGGCGATCGGTCGCGATAATGGTGTTCTGCTCTTTTTCTATTTGCTGCAAGACCGTGTTTAACGCCG‑CCTGGGTTTGCCACTCCCAGTACAGGCGGGCTACGCTGCCAGCCAGCAATTGGCGGG‑TTTGCT‑CG‑CG‑TTCCGCCGCCCGTGCt                                                                                                                                                                                                           <  2:1034789/162‑1 (MQ=255)
                                                                                        ttCTGATATAGCTGGCGATCGGTCGCGATAATGGTGTTCTGCTCTTTTTCTATTTGCTGCAAGACCGTGTTTAACGCCG‑CCTGGGTTTGCCACTCCCAGTACAGGCGGGCTACGCTGCCAGCCAGCAATTGGCGGG‑TTTGCT‑CG‑CG‑TTCCGCCGCCCGTGCt                                                                                                                                                                                                           >  1:1034789/1‑162 (MQ=255)
                                                                                                                  gATAATGGTGTTCTGCTCTTTTTCTATTTGCTGCAAGACCGTGTTTAACGCCG‑CCTGGGTTTGCCACTGACAGTACAGGCGGGCTACGCTGCCAGCCAGCAATTGGCGGG‑TTTGCT‑CG‑CG‑TTCCGCCGCCCGTGCTTTaa                                                                                                                                                                                                       <  1:1395702/140‑1 (MQ=255)
                                                                                                                           gtTCTGCTCTTTTTCTATTTGCTGCAAGACCGTGTTTAACGCCG‑CCTGGGTTTGCCACTCCCAGTACAGGCGGGCCACGCTGCCAGCCAGCAATTGGCGGG‑GTTGGT‑CC‑CG‑CTCCGCCCCCCGCGGCTTTACC‑CCACCCCGGCGGGGGGGAAACCCCCCCCGCTTC‑TTTCTCCCGGCAACCAGATGGCCGGCCGCC‑CCTAAGCCCAAAAGAACC‑CTGGGGTAACACGGGCCGGGCgca                                                                                        >  2:644733/1‑236 (MQ=255)
                                                                                                                            ttCTGCTCTTTTTCTATTTGCTGCAAGACCGTGTTTAACGCCG‑CCTGGGTTTGCCACTCCCAGTACAGGCGGGCTACGCTGCCAGCCAGCAATTGGCGGG‑GTTTCT‑CG‑CG‑TTCCCCCCCCCGTGCTTTAACC‑GTACCCAGGCGGGCAGTAACCTCCGCCCGCTTC‑TTTTCCCCGATATCGAGATGCCAGCCCCCC‑GGTAAA‑CCAAAAGTAACCTTTGGGTAACACCGGCCGGTCGTAc                                                                                       >  1:251556/1‑238 (MQ=255)
                                                                                                                                                        ctgttttcaaCGCCG‑CCGGGTTTTGCCACTCCCGGTCCGGGGGGGCTCCGCTGCCAGCCAGAAATTGGGGGG‑TTTCCC‑CG‑CG‑TCCCGCCGCCCGTTCTTTACCC‑GTCCCCGGGCGGGAGGTACCCCCCCCCCGATTC‑TTCCCCCGGATATGGAGATGCCAGCCCGCC‑GTTAAG‑CCAAAAGTACCGTTGGTGTACCACGGGCCGGTCGTACCTGCGGCCGGATCGTTC‑AGAG‑CA‑AACGGc                                                       <  2:322774/231‑1 (MQ=255)
                                                                                                                                                            gtTTAACCCCCCCCTGGTTTTGCCCCCCCCAGACCAGGCGGCTTCCGCTGCCCCCAGGCAATGGGGGGT‑TTTGCC‑GG‑CT‑TCCCCCCCCCTGTTTTTAACCC‑GTCCCCGGGCGGACAATACCCCCCCCCCGTTTC‑TTCCCCCGGATATCGAGAGGCCGCCCCGCC‑GTTAAG‑CCAAAAGTACCGTTGGTGTACCACGGGCCGGTCGTACCTGCGGCCGGATCGTTC‑AGAG‑Ca‑aa                                                           <  2:1299849/232‑1 (MQ=255)
                                                                                                                                                               tcaCGCCG‑CCTGGGTTTGCCCCCCCCCGGGCCGGCGGGCGCCGCGGGCAACCAGGAAGTGGGGGG‑GTTGGC‑CC‑CGTTTCCCCCGCCCG‑GGTTTAACCGGAACCGGGGGGGGCGGTACCCGCCGCCGAATCC‑TTCCCCCGGATAGCGGGAGGCCGGCCCGCC‑GTTAAG‑CCAAAAGTACCGTTGGTGTACCACGGGCCGGTCGTACCTGCGGCCGGATCGTTC‑AGAG‑CA‑AACGGCCCCAtt                                                 <  2:354397/237‑1 (MQ=255)
                                                                                                                                                                        ccTGGGTTTGCCACTCCCAGTACAGGCGGGCTACGCTTCCAGCCAGCAATTGGCGGG‑GTTTCT‑CGCCG‑TTCCCCCCCCCCGCCTTTACCC‑CTCCCACGGGGGGCGGAAAAC‑CCGCCCCGTTT‑TTTTCCCCCATATCTGCAGTCCCGCCCCCC‑CCTAAG‑CCCAAAAAACCCTTGGGGTATCCCCGGCCGGTGGTTCCTCCGGGCGGAGCCTTT‑CGAGACA‑AAAGGcccccctacaccttt                                         >  2:359653/1‑228 (MQ=255)
                                                                                                                                                                        ccTGGGTTTGCCACTCCCAGTACAGGCGGGCTACGCTGCCAGCCAGCAATTGGCGGG‑GTTGGT‑CG‑CG‑GTCCCCCCCCCCGGCTTTTAAC‑CCACCCCGGCGGGCGGGAAACCCCCCCCGCTTC‑TTTCCCCCCAAAACCAGAATCCCACCCCCC‑GGTAAA‑CCAAAAAAACCCTCGGTGGACCACGGGGCCGTCGCCCCCTCGGCCGGAGTGGTC‑ACAG‑CC‑AAAAGccccctccaga                                             >  2:1090676/1‑227 (MQ=255)
                                                                                                                                                                                  ccACTCCCAGTACAGGCGGGCTACGCTGCCAGCCAGCAATTGGCGGG‑GTTTTT‑CC‑CG‑TTTCCCCCCCCCTGCTTTTACC‑CCACCCCCGCGGGCAGGAACCCCCCCCCCCTTT‑TTTTCCCCGATATCTCGATGCCACCCCCCC‑CCTACG‑CCCAAAATACCCTTCGGGTGACACCGGCCCGGCGGGCCCTCCGCCCGGGCGCTT‑ACAG‑CACAACGGCCCCCTTAAACCTCCTCCCgcacct                               >  2:633999/1‑234 (MQ=255)
                                                                                                                                                                                      tCCCAGTACAGGCGGGCTACGCTGCCAGCCAGCAATTGGCGGG‑TTTTTC‑CC‑CG‑TTCCCCCGCCCCGGCTTTAACC‑CTCCCCAGGCGGGCGGTAACCCCCCCCCCATTCTTTTCCCCCAATA‑CGGGATGCCCGCCCCCC‑CGTAAC‑CCAAAAACACCCCTGGGGTACCCCGGCCCCGTCGCACCTCCGGCCGGTGCGTTC‑GTAG‑AC‑AACGGCCCCCTTAAGCCCGTTGCCGCCActtttt                           >  2:677605/1‑238 (MQ=255)
                                                                                                                                                                                       cccAGTACAGGGGGGCTCCGCGGCCAGCCAGCAATGGGCGGG‑TTTGCC‑CG‑CT‑TTCCCCCCCCCGTGCTTTACCC‑GTACCCAGGCGGGCAGTACCCTCCCCCCGATTC‑TTCCCCCAGATATCGAGATGCCAGCCCGCC‑GTTAAG‑CCAAAAGTACCGTTGGTGTACCACGGGCCGGTCGTACCTGCGGCCGGATCGTTC‑AGAG‑CA‑AACGGCCCCATTAAGCCTTCTGCCGACATTTTTTGc                         <  1:1070099/239‑1 (MQ=255)
                                                                                                                                                                                                 gCGGGCTACGCTGCCAGCCAGCAATTGGCGGG‑GTTGCT‑CG‑CG‑TTTCCCCGCCCCTGCTTTTAAC‑CTACCCCAGCGGGGCGTAACCCCCCCCCCATTC‑TTTTCCCCGAAATCCAGATGCCCGCCCCCC‑CGTAAA‑CCCAAAAAACCCGTGGGGTTCCCCCGGCCGGGCGCACCCTCGGGCGGGGTGTTT‑CTAG‑CA‑AAAGGCCCCCCTAAAACCTCTTCCCGCACTTTTTTTCGCTcccca                >  2:1070099/1‑235 (MQ=255)
                                                                                                                                                                                                    ggCTGCGCTGACAGCCAGCAATTGGCGGG‑TTTGCT‑CG‑CG‑TTCCGCCGCCCGTGCTTTAACC‑GTACCCAGGCGGGCAGTAACCTCCGCCCGATTC‑TTTCCCCAGATATCGAGATGc                                                                                                                                             <  1:1164415/115‑1 (MQ=255)
                                                                                                                                                                                                    ggCTACGCTGCCAGCCAGCAATTGGCGGGTTTTGCC‑CG‑GG‑TCCCCCCCCCCTGCCTTTACCC‑GAACCCGGGGGGGCGGAAACCCCCCCCCGGTTT‑TTTCCCCCGAAATCGGGA‑GCCCGCCCCCCGGTTAGC‑CCAAAAAAACCGTT‑GTGGTCCACGGGCCCGGCGTAACCCCCGCCGGGGCGTTCGAGAG‑CA‑AACGGCCCC‑CTAAACCCTCTTCCGCCCGTTTTTTCTGCTCCctattc             >  2:926501/1‑236 (MQ=255)
                                                                                                                                                                                                              ccagccagCAATTGGCGGG‑TTTTCT‑CG‑CG‑TTCCGCCGCCCGTGCTTTAACC‑GTACCCCGGCGGGCAGTAACCTCCGCCCGATTC‑TTTTCCCCGATATCGAGATGCCAGCCCGCC‑GGTAAG‑CCAAAAGTACCGTTTGTGTACCCCGGGCCGGTCGTACCTGCGGCCGGGTCGTTC‑CGAG‑CA‑AACGGCCCCCTTAAGCCTTCTTCCGCCCTTTTTTGCCGCTCCCTATTCCCCGAAAAGTc  >  2:895825/1‑239 (MQ=255)
                                                                                                                                                                                                              ccagccagCAATTGGCGGG‑TTTGCC‑CG‑CG‑TTCCGCCGCCCGGGCTTTAACC‑CTACCCCGGGGGGGCGTAACCCCCGCCCCCTTC‑TTTTCCCAGCTATCTAGGTGCCCGCccgcc‑g                                                                                                                                  >  2:1164415/1‑115 (MQ=255)
                                                                                                                                                                                                                                                   |                                                                                                                                                                                                                    
CATTTTCCCCGCGACATCGTTGAGCTGCTGCCGGGTTTTGCTGGCATTAATATCGGTTTCCACACCTTCAACTGAAGAAGTAATCCCGTTCTGATATAGCTGGCGATCGGTCGCGATAATGGTGTTCTGCTCTTTTTCTATTTGCTGCAAGACCGTGTTTAACGCCG‑CCTGGGTTTGCCACTCCCAGTACAGGCGGGCTACGCTGCCAGCCAGCAATTGGCGGG‑TTTGCT‑CG‑CG‑TTCCGCCGCCCGTGCTTTAACC‑GTACCCAGGCGGGCAGTAACCTCCGCCCGATTC‑TTTCCCCAGATATCGAGATGCCAGCCCGCC‑GTTAAG‑CCAAAAGTACCGTTGGTGTACCACGGGCCGGTCGTACCTGCGGCCGGATCGTTC‑AGAG‑CA‑AACGGCCCCATTAAGCCTTCTGCCGACATTTTTTGCCGCTCCATATCCGCCGAAAAGTC  >  NC_000913/2227998‑2228441

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑