Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,037,4960AT33.3% 18.0 / 27.1 30intergenic (+161/‑23)alaT/rrlAtRNA‑Ala/23S ribosomal RNA of rrnA operon
Reads supporting (aligned to +/- strand):  ref base A (18/2);  new base T (4/6);  total (22/8)
Fisher's exact test for biased strand distribution p-value = 7.23e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.97e-04
Rejected as consensus: Frequency below/above cutoff threshold.

AAAAAATACTTCAGAGTGTACCTGCAAAGGTTCACTGCGAAGTTTTGCTCTTTAAAAATCTGGATCAAGCTGAAAATTGAAACACTGAACAACGAAAGTTGTTCGTGAGTCTCTCAAATTTTCGCAACACGATGATGAATCGAAAGAAACATCTTCGGGTTGTGAGGTTAAGCGACTAAGCGT  >  NC_000913/4037354‑4037536
                                                                                                                                              |                                        
aaaaaaTACTTCAGAGTGTACCTGCAAAGGTTCACTGCGAAGTTTTGCTCTTTAAAAATCTGGATCAAGCTGAAAATTGAAACACTGAACAACGAAAGTTGTTCGTGAGTCTCTCAAATTTTCGCAACACGATGATGAATAga                                          >  1:99858/1‑143 (MQ=25)
   aaaTATTTCAGAGTGTACCTGCAAAGGTTCACTGCGAAGTTTTGCTCTTTAAAAATCTGGATCAAGCTGAAAATTGAAACACTGAACAACGAAAGTTGTTCGTGAGTCTCTCAAATTTTCGCAACACGATGATGAATCgaaag                                       <  2:531283/143‑1 (MQ=38)
     aTACTTCAGAGTGTACCTGCAAAGGTTCACTGCGAAGTTTTGCACTTTAAAAATCTGTATCAAGCTGAAAATTGAAACACTGAACAACGAAAGTTGTTCGTGAGTCTCTCAAATTTTCGCAACACGATGATGAATCgtaagaa                                     <  1:415493/143‑1 (MQ=255)
      tACTTCAGAGTGTACCTGCAAAGGTTCACTGCGAAGTTTTGCTCTTTAAAAATCTGGATCAAGCTGAAAATTGAAACACTGAACAACGAAAGTTGTTCGTGAGTCTCTCAAATTTTCGCAACACGATGATGAATCgtaagaaa                                    <  2:688633/143‑1 (MQ=25)
      gacgtCAGGGTGTACCTGCAAAGGTTCACTGCGAAGTTTTGCTCTTTAAAAATCTGGATCAAGCTGAAAATTGAAACACTGAACAACGAAAGTTGTTCGTGAGTCTCTCAAATTTTCGCAACACGATGATGAATCgtaagaaa                                    <  2:906507/139‑1 (MQ=255)
       gcTTCAGGGGGGACCTGCAAAGGTGCACTGGGAAGTTTTGCTGTTGAAAGATCTGGATCAAGCTGAAGATGGAAACACTGAACAACGAAAGTTGTTCGTGAGTCTCTCAAATTTTCGCAACACGATGATGAATCGTAAGAAAc                                   <  2:766180/142‑1 (MQ=11)
       aCTTGAGCGTGGACCTGCAAAGGTTCAGTGCGAAGTTTTGCTCTTTCAAATTCTGGATCAAGCTGAAAATTGAAACATTGAACAACGAAAGTTGTTCGTGAGTCTCTCAAATTTTCGCAACACGATGATGAATCGTAAGAAAc                                   <  2:850962/143‑1 (MQ=11)
       aCTTCGGAGTGTACCTGCAAAGGTTCACTGCGACGTTTTGCTCTTTAAAAATCTGGATCAAGCTGAGAATTGGGGCACTGAACAACGAAAGTTGTTCGTGAGTCTCTCAAATTTTCGCAACACGATGATGAATCGTAAGAAAc                                   <  2:439563/143‑1 (MQ=11)
         ttCAGAGTGTACCTGCAAAGGTTCACTGCGAAGTTTTGCTCTTTAAAAATCTGGATCAAGCTGAAAATTGAAACACTGAACAACGAAAGTTGTTCGTGAGTCTCTCAAATTTTCGCAACACGATGATGAATCGAAAGAAACAt                                 >  1:771206/1‑143 (MQ=37)
         ttCAGAGTGTACCTGCAAAGGTTCACTGCGAAGTTTTGCTCTTTAAAAATCTGGATCAAGCTGAAAATTGAAACACTGAACAACGAAAGTTGTTCGTGAGTCTCTCAAATTTTCGCAACACGATGATGAATCGAAAGAAACAt                                 >  2:128190/1‑143 (MQ=38)
         ttCAGAGTGTACCTGCAAAGGTTCACTGCGAAGTTTTGCTCTTTAAAAATCTGGATCAAGCTGAAAATTGAAACACTGAACAACGAAAGTTGTTCGTGAGTCTCTCAAATTTTCGCAACACGATGATGAATCGAAAGAAACAt                                 >  1:794669/1‑143 (MQ=38)
         ttCAGAGTGTACCTGCAAAGGTTCACTGCGAAGTTTTGCTCTTTAAAAATCTGGATCAAGCTGAAAATTGAAACACTGAACAACGAAAGTTGTTCGTGAGTCTCTCAAATTTTCGCAACACGATGAGCAATCGAAAGAAACAt                                 >  2:413895/1‑143 (MQ=255)
          tCAGAGTGTACCTGCAAAGGTTCACTGCGAAGTTTTGCTCTTTAAAAATCTGGATCAAGCTGAAAATTGAAACACTGAACAACGAAAGTTGTTCGTGAGTCTCTCAAATTTTCGCAACACGATGATGAATCGAAAGAAACATc                                >  2:166901/1‑143 (MQ=38)
            agagTGTACCTGCAAAGGTTCACTGCGAAGTTTTGCTCTTTAAAAATCTGGATCAAGCTGAAAATTGAAACACTGAACAACGAAAGTTGTTCGTGAGTCTCTCAAATTTTCGCGACACGATGCTGCATCGTAAGAAACGTCtt                              >  1:853824/1‑143 (MQ=11)
            agagTGTACCTGCAAAGGTTCACTGCGAAGTTTTGCTCTTTAAAAATCTGGATCAAGCTGAAAATTGAAACACTGAACAACGAAAGTTGTTCGTGAGTCTCTCAAATTTTCGCAACACGATGATGAATCGTAAGAACCATCtt                              >  2:652463/1‑143 (MQ=25)
            agagTGTACCTGCAAAGGTTCACTGCGAAGTTTTGCTCTTGGAAAATCTGGATCAAGCTGAAAATTGAAACACTGAACAACGAAAGTTGTTCGTGAGTCTCTCAAATTTTCGCAACACGATGATGAATCGTAAGACACATCtt                              >  1:815294/1‑143 (MQ=255)
               gtgtACCTGCAAAGGTTCACTGCGAAGTTTTGCTCTTTAAAAATCTGGATCAAGCTGAAAATTGAAACACTGAACAACGAAAGTTGTTCGTGAGTCTCTCAAATTTTCGCAACACGATGATGAATCGTAAGAAACATCTTCgg                           <  2:805797/143‑1 (MQ=25)
               gtgtACCTGCAAAGGTTCACTGCGAAGTTTTGCTCTTTAAAAATCTGGATCAAGCTGAAAATTGAAACACTGAACAACGAAAGTTGTTCGTGAGTCTCTCAAATTTTCGCAACACGATGATGAATCGAAAGAAACATCTTCgg                           <  2:458928/143‑1 (MQ=39)
                tgtACCTGCAAAGGTTCACTGCGAAGCTTAGCTCATTTGTAATCGGAATCAAGCTGAAAATTGAAACACTGAACAACGAAAGTTGTTCGTGAGTCTCTCAAATTTTCGCAACACGATGATGAATCGAAAGCAACATCTCCggg                          >  1:863682/1‑143 (MQ=11)
                  tACCTGCAAAGGTTCACTGCGAAGTTTTGCTCTTTAAAAATCTGGATCAAGCTGAAAATTGAAACACTGAACAACGAAAGTTGTTCGTGAGTCTCTCAAATTTTCGCAACACGATGATGAATCGAAAGAAACATCTTCGGGtt                        <  1:77316/143‑1 (MQ=38)
                    ccTGCAAAGGTTGACTGCGAAGTTTTGGTCGTTAAAAATCTGGATCAAGCTGAAAATTGAAACACTGAACAACGAAAGTTGTTCGTGAGTCTCTCAAATTTTCGCAACACGATGATGAATCGTAAGAAACATCTTCGGGTtgt                      <  2:246979/143‑1 (MQ=255)
                     cTGCAAAGGTTCACTGCGAAGTTTTGCTCTTTAAAAATCTGGATCAAGCTGAAAATTGAAACACTGAACAACGAAAGTTGTTCGTGAGTCTCTCAAATTTTCGCAACACGATGATGAATCGAAAGAAACATCTTCGGCTtgtg                     >  2:416347/1‑143 (MQ=37)
                     cTGCAAAGGTTCACTGCGAAGTTTTGCTCTTTAAAAATCTGGATCAAGCTGAAAATTGAAACACTGAACAACGAAAGTTGTTCGTGAGTCTCTCAAATTTTAGCAATTCGATGATGAATCGAAAGAAACATCTTCGGgtggtg                     >  1:855597/1‑143 (MQ=255)
                      tGCAAAGGTTCACTGCGAAGTTTTGCTCTTTAAAAATCTGGATCAAGCTGAAAATTGAAACACTGAACAACGAAAGTTGTTCGTGAGTCTCTCAAATTTTCGCAACACGATGATGAATCGTAAGAAACATCTTCGGGTTGTGa                    <  1:101508/143‑1 (MQ=25)
                       gCAAAGGTTCACTGCGAAGTTTTGCTCTTTAAAAATCTGGATCAAGCTGAAAATTGAAACACTGAACAACGAAAGTTGTTCGTGAGTCTCTCAAATTTTCGCAACACGATGATGAATCGAAAGAAACATCTTCGGGTTGTGAg                   >  1:272724/1‑143 (MQ=37)
                             gTTCACTGCGAAGTTTTGCTCTTTAAAAATCTGGATCAAGCTGAAAATTGAAACACTGAACAACGAAAGTTGTTCGTGAGTCTCTCAAATTTTCGCAACACGATGATGAATCGAAAGAAACATCTTCGGGTTGTGAGGTTAAg             >  1:169655/1‑143 (MQ=38)
                              ttCACTGCGAAGTTTTGCTCTTTAAAAATCTGGATCAAGCTGAAAATTGAAACACTGAACAACGAAAGTTGTTCGTGAGTCTCTCAAATTTTCGCAACACGATGATGAATCGAAAGAAACATCTTCGGGTTGTGAGGTTCAGc            >  1:393695/1‑143 (MQ=38)
                                 aCTGCGAAGTTTTGCTCTTTAAAAATCTGGATCAAGCTGAAAATTGAAACACTGAACAACGAAAGTTGTTCGTGCGTCTCTCACATTTTCGCAACCCGATGATGACTCGTACGCAACATCTTCGGGTTGTGAGGTTAACCGAc         >  1:838515/1‑143 (MQ=11)
                                   tGCGAAGTTTTGCTCTTTAAAAATCTGGATCAAGCTGAAAATTGAAACACTGAACAACGAAAGTTGTTCGTGAGTCTCTCAAATTTTCGCAACACGATGATGAATCGAAAGAAACATCTTCGGGTTGTGAGGTTAAGCGACTa       >  1:43765/1‑143 (MQ=35)
                                   tGCGAAGTTTTGCTCTTTAAAAATCTGGATCAAGCTGAAAATTGAAACACTGAACAACGAAAGTTGTTCGTGAGTCTCTCAAATTTTCGCAACACGATGATGAATCGAAAGAAACATCTTCGGGTGGTGAGGTTAAGCGACTa       >  1:445505/1‑143 (MQ=25)
                                   tGCGAAGTTTTGCTCTTTAAAAATCTGGATCAAGCTGAAAATTGAAACACTGAACAACGAAAGTTGTCCGTGAGTCGCTCAAATTTTCGCAACACGATTATGAATCGAAAGAAACATCTTCCGGATGCGAGGTCAAGCGACTa       >  2:147626/1‑143 (MQ=11)
                                    gCGAAGTTTTGCTCTTTAAAAATCTGGATCAAGCTGAAAATTGAAACACTGAACAACGAAAGTTGTTCGTGAGTCTCTCAAATTTTCGCAACACGATGATGAATCGAAAGAAACATCTTCGGGTTGTGCGGTTAAGCGACTaa      >  1:542306/1‑143 (MQ=25)
                                    gCGAAGTTTTGCTCTTTAAAAATCTGGATCAAGCTGAAAATTGAAACACTGAACAACGAAAGTTGTTCGTGAGTATCTCAAATTTTCGCAACACGATGATGAATCGAAAGAAACATCTTCGGGTTGTGAGGTTAAGCGACTaa      >  1:156988/1‑143 (MQ=25)
                                     cGAAGTTTTGCTCTTTAAAAATCTGGATCAAGCTGAAAATTGAAACACTGAACAACGAAAGTTGTTCGTGAGTCTCTCAAATTTTCGCAACACGATGATGAATCGAAAGAAACATCTTCGGGTTGGGAGGTTAAGCGACTAAg     >  1:5699/1‑143 (MQ=21)
                                        aGTTTTGCTCTTTAAAAATCTGGATCAAGCTGAAAATTGAAACACTGAACAACGAAAGTTGTTCGTGAGTCTCTCAAATTTTCGCAACACGATGCTGAATCGAAAGAAACATCTTCGGGTTGTAAAGATAAGCGACTAAGAGt  >  1:177525/1‑143 (MQ=11)
                                                                                                                                              |                                        
AAAAAATACTTCAGAGTGTACCTGCAAAGGTTCACTGCGAAGTTTTGCTCTTTAAAAATCTGGATCAAGCTGAAAATTGAAACACTGAACAACGAAAGTTGTTCGTGAGTCTCTCAAATTTTCGCAACACGATGATGAATCGAAAGAAACATCTTCGGGTTGTGAGGTTAAGCGACTAAGCGT  >  NC_000913/4037354‑4037536

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑