Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,228,2750TC53.1% 25.5 / 38.3 32pseudogene (335/1287 nt)mdtQpseudogene; putative channel/filament proteins
Reads supporting (aligned to +/- strand):  ref base T (7/8);  new base C (3/14);  total (10/22)
Fisher's exact test for biased strand distribution p-value = 1.28e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.72e-05

GCTCTTTTTCTATTTGCTGCAAGACCGTGTTTAACGCCGCCTGGGTTTGCCACTCCCAGTACAGGCGGGCTACGCTGCCAGCCAGCAATTGGCGGGTTTGCTCGCGTTCCGCCGCCCGTGCTTTAACCGTACCCAGGCGGGCAGTAACCTCCGCCCGATTCTTTCCCCAGATATCGAGATGCCAGCCCGCCGTTAAGCCAAAAGTACCGTTGGTGTACCACGGGCCGGTCGTACCTGCGGCCGGATCGTTCAGAGCAAACGGCCCCATTAAGCCTTCTGCCGACATTTT  >  NC_000913/2228126‑2228414
                                                                                                                                                     |                                                                                                                                           
gCTCTTTTTCTATTTGCTGCAAGACCGTGTTTAACGCCGCCTGGGTTTGCCACTCCCAGTACAGGCGGGCTACGCTGCCAGCCAGCAATTGGCGGGTTTGCTCGCGTTCCGCCGCCCGTGCTTTAACCGTACCCAGGCGGGCAGTAACCTc                                                                                                                                            <  2:264439/151‑1 (MQ=255)
                   cAAGACCGTGTTTAACGCCGCCTGGGTTTGCCACTCCCAGTACAGGCGGGCTACGCTGCCAGCCAGCAATTGGCGGGTTTGCTCGCGTTCCGCCGCCCGTGCTTTAACCGTACCCAGGCGGGCAGTAACCTCCGCCCGATTCTTTCCCCAg                                                                                                                         <  1:393147/151‑1 (MQ=255)
                   cAAGACCGTGTTTAACGCCGCCTGGGTTTGCCACTCCCAGTACAGGCGGGCTACGCTGCCAGCCAGCAATTGGCGGGTTTGCTCGCGTTCCGCCGCCCGTGCTTTAACCGTACCCAGGCGGGCAGTAACCTCCGCCCGATTCTTTCCCCAg                                                                                                                         <  1:688475/151‑1 (MQ=255)
                    aaGACCGTGTTTAACGCCGCCTGGGTTTGCCACTCCCAGTACAGGCGGGCTACGCTGCCAGCCAGCAATTGGCGGGGTTGCTCGCGTTCCGCCCCCCGTGCTTTTACCGGACCCCGGCGGGGCGGAACCCCCCCCCCGTTCTTTtccc                                                                                                                           >  1:776024/1‑148 (MQ=255)
                       aCCGTGTTTAACGCCGCCTGGGTTTGCCACTCCCAGTACAGGCGGGCTACGCTGCCAGCCAGCAATTGGCGGGGTTGCTCGCGTTCCGCCCCCCCTGCTTTTACCGGACCCCGGCGGGGGGGAACCTCCGCCCGATTTTTTTCCCCGatat                                                                                                                     >  2:100728/1‑151 (MQ=255)
                            gtTTAACGCCGCCTGGGTTTGCCACTCCCAGTACAGGCGGGCTACGCTGCCAGCCAGCAATTGGCGGGTTTGCTCGCGTTCCGCCGCCCGTGCTTTAACCGTACCCAGGCGGGCAGTAACCTCCGCCCGATTCTTTCCCCAGATATCgaga                                                                                                                <  2:158072/151‑1 (MQ=255)
                              ttAACGCCGCCTGGGTTTGCCACTCCCAGTACAGGCGGGCTACGCTGCCAGCCAGCAATTGGCGGGTTTGCTCGCGTTCCGCCCCCCGCGCTTTAATCCTACCCCAGCGGGGAGGAACACCCCCCCGATTTTTTTCCCTGATATCGAGATg                                                                                                              >  1:106219/1‑151 (MQ=255)
                              ttAACGCCGCCTGGGTTTGCCACTCCCAGTACAGGCGGGCTACGCTGCCAGCCAGCAATTGGCGGGGTTTCTCGCGTTCCGCCGCCCGTGCTTTTACCGTACCCCGGCGGGCAGTAACCCCCGCCCCATTCTTTTCCCCGATATCgaga                                                                                                                >  1:398150/1‑149 (MQ=255)
                                  cgccgcCTGGGTTTGCCACTCCCAGTACAGGCGGGCTACGCTGCCAGCCAGCAATTGGCGGGTTTGCTCGCGTTCCGCCGCCCGTGCTTTAACCGTACCCAGGCGGGCAGTAACCTCCGCCCGATTCTTTCCCCAGATATCGAGATGCCAg                                                                                                          <  2:718231/151‑1 (MQ=255)
                                    ccgccTGGGTTTGCCACTCCCAGTACAGGCGGGCTACGCTGCCAGCCAACAATTGGCGGGTTTGCTCCCGTTCCCCCGCCCCGGCTTTAAACGTACCCAAGCGGGGAGGAACCTCCCCCCCAGTTTTTcccccggtaaacggat                                                                                                               >  1:589477/1‑132 (MQ=255)
                                     cgccTGGGTTTGCCACTCCCAGTACAGGCGGGCTACGCTGCCAGCCAGCAATTGGCGGGTTTGCTCGCGTTCCGCCGCCCGTGCTTTAACCGTACCCAGGCGGGCAGTAACCTCCGCCCGATTCTTTCCCCAGATATCGAGATGCCAGccc                                                                                                       <  1:573201/151‑1 (MQ=255)
                                          gggTTTGCCACTCCCAGTACAGGCGGGCTACGCTGCCAGCCAGCAATTGGCGGGTTTGCTCGCGTTCCGCCGCCCGTGCTTTAACCGTACCCAGGCGGGCAGTAACCTCCGCCCGATTCTTTCCCCAGATATCGAGATGCCAGCccgccg                                                                                                   <  1:663440/150‑1 (MQ=255)
                                             tttGCCACTCCCAGTACAGGCGGGCTACGCTGCCAGCCAGCAATTGGCGGGTTTTCTCGCGGTCCGCCGCCCGCGCTTTTACCGTTCCCCGGCGGGCAGTAACCTCCCCCCCATTCTTTTCCCCGAAATCGAGATGGCcgcccgcccct                                                                                                 >  1:20879/1‑146 (MQ=255)
                                                    cTCCCAGTACAGGCGGGCTCCGCTGCCAGCCAGCAATGGGCGGGTTTGCTCGCGTTCCGCCGCCCGTGTTTTACCCGTCCCCGGGCGGGCAGTACCCCCCCCCCGATTCTTTCCCCAGATATCGAGATGCCAGCCCGCCGTTAAGCCaaa                                                                                         <  1:757525/150‑1 (MQ=255)
                                                          gTACAGGCGGGCTTCGTTCCCGACCAGAAATTGGCTGTTTTGCTCGCTTTCCCCCCCCCTTTTTTTACCCGTACCCGGGGGGGAAATAACCCCCGCCCGATTTTTTCCCCAGATACGGAGATGCCAGCCCGCCGTTAAGCCAAAAGTAcc                                                                                   <  1:505504/150‑1 (MQ=255)
                                                           tACGGGCGGGCTACGCTGCCAGCCAGCAATTGGCGGGTTTGCTCGCGTTCCGCCGCCCGTGCTTTACCCGTCCCCAGGCGGGCAGAACCCTCCGCCCGATTCTTTCCCCAGATATCGAGATGCCAGCCCGCCGTTAAGCCAAAAGTAc                                                                                    <  1:750066/148‑1 (MQ=255)
                                                              aGGCGGGCTACGCTGCCAGCCAGCAATTGGCGAGTTTGCTCGCGTTCCGCCGCCCGTGCTTTAACCGTACCCAGGCGGGCAGTAACCTCCGCCCGATTCTTTCCCCAGATATCGAGATGCCAGCCCGCCGTTAAGCCAAAAGTACCGTTgg                                                                              >  1:788410/1‑151 (MQ=255)
                                                                gCGGGTTCCGCTGCCAGCCAGCAATGGGCGGGTTTGCTCGCGTCCCCCCGCCCGTGTTTTAACCGTCCCCAGGGGGGCAGTACCCCCCGCCCGATTTTTTCCCCAGATATCGAGATGCCAGCCCGCCGTTAAGCCAAAAGTACCGTTGgtg                                                                            <  1:461895/151‑1 (MQ=255)
                                                                             ccagccagCAATGGGGGGGTTTGCTCGCGTCCCGCCCCCCGTGCTTTACCCGTCCCCAGGCGGGCAGTACCCCCCGCCCGATTCTTCCCCCAGATATCGAGATGCCAGCCCGCCGTTAAGCCAAAAGTACCGTTGGTGTACCACGGGcc                                                                 <  2:775958/149‑1 (MQ=255)
                                                                                      aaTTGGCGGGTTTGCCCGCGTCCCGCCCCCCGTGTTTTACCCGTCCCCAGGCGGGCAGTACCCCCCGCCCGATTCTTCCCCCAGATATCGAGATGCCAGCCCGCCGTTAAGCCAAAAGTACCGTTGGTGTACCACGGGCCGGTCGTACCTg                                                      <  2:685848/151‑1 (MQ=255)
                                                                                             gggTTTGCTCGCGTTCCGCCGCCCGTGCTTTAACCGTACCCAGGCGGGCAGTAACCTCCGCCCGATTCTTTCCCCAGATATCGAGATGCCAGCCCGCCGTTAAGCCAAAAGTACCGTTGGTGTACCACGGGCCGGTCGTACCTGCGGCCgg                                               >  1:35585/1‑151 (MQ=255)
                                                                                                tgtcccggcttcccgcccCCCGTGCTTTACCCGTACCCAGGGGGGAAGTACCCCCCGCCCGATTCTTTCCCCAGATATCGAGAGGCCAGCCCGCCGTTAAGCCAAAAGTACCGTTGGTGTACCACGGGCCGGTCGTACCTGCGGCCGGAt                                             <  2:761517/138‑1 (MQ=255)
                                                                                                   gCTCGCGTTCCGCCGCCCGTGCTTTAACCGTACCCAGGCGGGCAGTAACCTCCGCCCGATTCTTTCCCCAGATATCGAGATGCCAGCCCGCCGTTAAGCCAAAAGTACCGTTGGTGTACCACGGGCCGGTCGTACCTGCGGCCGGATCGtt                                         >  1:240242/1‑151 (MQ=255)
                                                                                                    cTCCCGTTCCGCCCCCCGTTTTTTACCCGTCCCCGGGGGGGAAGTACCCCCCGCCCGTTTCTTCCCCCAGATATCGAGAGGCCAGCCCGCCGTTAAGCCAAAAGTACCGTTGGTGTACCACGGGCCGGTCGTACCTGCGGCCGGATCg                                           <  2:577095/148‑1 (MQ=255)
                                                                                                            ccgcccCCCGTGTTTTAACCGTCCCGAGGGGGGCAGAACCCCCCCCCCGTTTCTTCCCCCAGATATCGGGAGGCCAGCCCGCCGTTAAGCCAAAAGTACCGTTGGTGTACCACGGGCCGGTCGTACCTGCGGCCGGATCGTTCAGAGCa                                  <  2:273219/149‑1 (MQ=255)
                                                                                                               ccgccCGTGCTTTACCCGTCCCCAGGCGGGCAGTACCCCCCGCCCGATTCTTTCCCCAGATATCGAGATGCCAGCCCGCCGTTAAGCCAAAAGTACCGTTGGTGTACCACGGGCCGGTCGTACCTGCGGCCGGATCGTTCAGAGCAAACgg                             <  1:576146/151‑1 (MQ=255)
                                                                                                                   ccGTGCTTTAACCGTACCCAGGCGGGCAGTAACCTCCGCCCGATTCTTTCCCCAGATATCGAGATGCCAGCCCGCCGTTAAGCCAAAAGTACCGTTGGTGTACCACGGGCCGGTCGTACCTGCGGCCGGATCGTTCAGAGCAAACGGcccc                         >  1:722482/1‑151 (MQ=255)
                                                                                                                        cTTTACCCTTACCCGGGCGGGCAGTACCCCCCGCCCTTTTCTTCCCCCAGATATCGAGATGCCAGCCCGCCGTTAAGCCAAAAGTACCGTTGGTGTACCACGGGCCGGTCGTACCTGCGGCCGGATCGTTCAGAGCAAACGGCCCCa                        <  2:759784/147‑1 (MQ=255)
                                                                                                                         tttAACCGTCCCCGGGGGGGCAGTACCCCCCCCCCGATTTTTCCCCCAGATAGCGAGATGCCGGCCCGCCGTTAAGCCAAAAGTACCGTTGGTGTACCACGGGCCGGTCGTACCTGCGGCCGGATCGTTCAGAGCAAACGGCCCCATTaa                    <  1:311265/150‑1 (MQ=255)
                                                                                                                         tttAACCGTCCCCAGGCGGGCAGTACCCCCCGCCCGATTCTTCCCCCAAATATCGAGATGCCAGCCCGCCGTTAAGCCAAAAGTACCGTTGGTGTACCACGGGCCGGTCGTACCTGCGGCCGGATCGTTCAGAGCAAACGGCCCCAt                       <  1:619610/147‑1 (MQ=255)
                                                                                                                                   cccGGGGGGGAAGTACCCCCCCCCCTATTCTTCCCCCAGATACCGAGTTGCCAGCCCGCCGTTAAGCCAAAAGTACCGTTGGTGTACCACGGGCCGGTCGTACCTGCGGCCGGATCGTTCAGAGCAAACGGCCCCATTAAGCCTTCTGCCg         <  2:280057/151‑1 (MQ=255)
                                                                                                                                          gggCAATACCCCCCCCCCGTTTCTTCCCCCAGATATCGAGTCGCCAGCCCGCCGTTAAGCCAAAAGTACCGTTGGTGTACCACGGGCCGGTCGTACCTGCGGCCGGATCGTTCAGAGCAAACGGCCCCATTAAGCCTTCTGCCGACAtttt  <  2:93043/151‑1 (MQ=255)
                                                                                                                                                     |                                                                                                                                           
GCTCTTTTTCTATTTGCTGCAAGACCGTGTTTAACGCCGCCTGGGTTTGCCACTCCCAGTACAGGCGGGCTACGCTGCCAGCCAGCAATTGGCGGGTTTGCTCGCGTTCCGCCGCCCGTGCTTTAACCGTACCCAGGCGGGCAGTAACCTCCGCCCGATTCTTTCCCCAGATATCGAGATGCCAGCCCGCCGTTAAGCCAAAAGTACCGTTGGTGTACCACGGGCCGGTCGTACCTGCGGCCGGATCGTTCAGAGCAAACGGCCCCATTAAGCCTTCTGCCGACATTTT  >  NC_000913/2228126‑2228414

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑