Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*REL6062,631,7720AC39.5% 64.3 / 19.2 43intergenic (‑267/‑141)rpoE/nadBRNA polymerase, sigma 24 (sigma E) factor/L‑aspartate oxidase
Reads supporting (aligned to +/- strand):  ref base A (21/5);  new base C (0/17);  total (21/22)
Fisher's exact test for biased strand distribution p-value = 7.67e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

TATCTGTGTAGAAATGCCCATTTAACTGCCTGAAGAGTAACCCAACGGCCTTTTTATTTCACCACCTAATCCTCCACCAGCCAGTAACTTCTCTTTTTCTCGCCGCCCTGCGTCAGCGTGTTTAGCCACTGTAACAAATATTAAAAT  >  REL606/2631697‑2631843
                                                                           |                                                                       
tATCTGTGTAGAAATGCCCATTTAACTGCCTGAAGAGTAACCCAACGGCCTTTTTATTTCACCACCTAATCCTcca                                                                         <  1:1049259/76‑1 (MQ=255)
tATCTGTGTAGAAATGCCCATTTAACTGCCTGAAGAGTAACCCAACGGCCTTTTTATTTCACCACCTAATCCTcca                                                                         <  1:287305/76‑1 (MQ=255)
  tCTGTGTAGAAATGCCCATTTAACTGCCTGAAGAGTAACCCAACGGCCTTTTTATTTCACCACCTAATCCTccacc                                                                       <  2:732816/76‑1 (MQ=255)
    tgtgTAGAAATGCCCATTTAACTGCCTGAAGAGTAACCCAACGGCCTTTTTATTTCACCACCTAATCCTCCAccag                                                                     <  1:735868/76‑1 (MQ=255)
      tgtAGAAATGCCCATTTAACTGCCTGAAGAGTAACCCAACGGCCTTTTTATTTCACCACCTAATCCTCCAccagcc                                                                   >  1:1311927/1‑76 (MQ=255)
        tAGAAATGCCCATTTAACTGCCTGAAGAGTAACCCAACGGCCTTTTTATTTCACCACCTAATCCTCCAccagccag                                                                 <  1:869316/76‑1 (MQ=255)
           aaaTGCCCATTTAACTGCCTGAAGAGTAACCCAACGGCCTTTTTATTTCACCACCTAATCCTCCACCAGCCAGTaa                                                              >  1:395276/1‑76 (MQ=255)
           aaaTGCCCATTTAACTGCCTGAAGAGTAACCCAACGGCCTTTTTATTTCACCACCTAATCCTCCACCAGCCAGTaa                                                              >  1:1705031/1‑76 (MQ=255)
               gCCCATTTAACTGCCTGAAGAGTAACCCAACGGCCTTTTTATTTCACCCCCTAATCCTCCCCCAGCCAGTAACTtc                                                          <  2:378423/76‑1 (MQ=255)
                   aTTTAACTGCCTGAAGAGTAACCCAACGGCCTTTTTATTTCACCACCTAATCCTCCACCAGCCAGTAACTTCTCtt                                                      >  2:1174851/1‑76 (MQ=255)
                      tAACTGCCTGAAGAGTAACCCAACGGCCTTTTTATTTCCCCACCTAACCCCCCCCCAGCCAGTAACTTCTCttttt                                                   <  2:518781/76‑1 (MQ=255)
                       aaCTGCCTGAAGAGTAACCCAACGGCCTTTTTATTTCACCACCTAATCCTCCACCAGCCAGTAACTTCTCTTTTtc                                                  >  1:217766/1‑76 (MQ=255)
                        aCTGCCTGAAGAGTAACCCAACGGCCTTTTTATTTCCCCACCTAATCCCCCCCCAGCCAGTAACTTCTCTTTTtct                                                 <  2:1287067/76‑1 (MQ=255)
                           gCCTGAAGAGTAACCCAACGGCCTTTTTATTTCACCACCTAATCCTCCACCAGCCAGTAACTTCTCTTTTTCTcgc                                              >  2:1041611/1‑76 (MQ=255)
                              tGAAGAGTAACCCAACGGCCTTTTTATTTCACCACCTAATCCTCCACCAGCCAGTAACTTCTCTTTTTCTcgccgc                                           >  1:1670448/1‑76 (MQ=255)
                               gAAGAGTACCCCAACGGCCTTTTTATTTCACCCCCTAATCCTCCACCAGCCAGTAACTTCTCTTTTTCTCgccgcc                                          <  2:853082/76‑1 (MQ=255)
                               gAAGAGTAACCCAACGGCCTTTTTATTTCACCACCTAATCCTCCACCAGCCAGTAACTTCTCTTTTTCTCgccgcc                                          >  1:1009728/1‑76 (MQ=255)
                                aaGAGTAACCCAACGGCCTTTTTATTTCACCACCTAATCCTCCACCAGCCAGTAACTTCTCTTTTTCTCGCCGccc                                         >  2:990591/1‑76 (MQ=255)
                                aaGAGTAACCCAACGGCCTTTTTATTTCACCACCTAATCCTCCACCAGCCAGTAACTTCTCTTTTTCTCGCCGccc                                         >  1:254827/1‑76 (MQ=255)
                                 agagTAACCCAACGGCCTTTTTATTTCACCACCTAATCCTCCACCAGCCAGTAACTTCTCTTTTTCTCGCCGCCCt                                        >  2:1059144/1‑76 (MQ=255)
                                  gagTAACCCAACGGCCTTTTTATTTCCCCCCCTAATCCCCCACCAGCCAGTAACTTCTCTTTTTCTCGCCGCCCTg                                       <  2:206170/76‑1 (MQ=255)
                                  gagTAACCCAACGGCCTTTTTATTTCCCCACCTAACCCTCCCCCAGCCAGTAACTTCTCTTTTTCTCGCCGCCCTg                                       <  1:438972/76‑1 (MQ=255)
                                  gagTAACCCAACGGCCTTTTTATTTCACCACCTAATCCTCCACCAGCCAGTAACTTCTCTTTTTCTCGCCGCCCTg                                       >  1:284774/1‑76 (MQ=255)
                                  gagTAACCCAACGGCCTTTTTATTGCACCCCCTAATCCTCCCCCAGCCAGTAACTTCTCTTTTTCTCGCCGCCCTg                                       <  1:95684/76‑1 (MQ=255)
                                  gaatAACCCAACGGCTTTTTTATTTCCCCCCCTAACCCCCCACCAGCCAGTAACTTCTCTTTTTCTCGCCGCCCTg                                       <  2:1165210/73‑1 (MQ=255)
                                      aaCCCAACGGCCTTTTTATTTCACCACCTAATCCTCCACCAGCCAGTAACTTCTCTTTTTCTCGCCGCCCTGCGTc                                   >  2:137956/1‑76 (MQ=255)
                                      aaCCCAACGGCCTTTTTATTTCACCACCTAATCCTCCACCAGCCAGTAACTTCTCTTTTTCTCGCCGCCCTGCGTc                                   >  1:1685886/1‑76 (MQ=255)
                                        cccAACGGCTTTTTTATTTCACCACCTAACCCCCCCCCAGCCAGTAACTTCTCTTTTTCTCGCCGCCCTGCGTCAg                                 <  1:911758/76‑1 (MQ=255)
                                        cacAACGGCCTTTTTATTACACACCCCAACCCCCCCCCAGCCAGTAACTTCTCTTTTTCTCGCCGCCCTGCGTCAg                                 <  1:911729/74‑1 (MQ=255)
                                            aCGGCCTTTTTATTTCACCCCCTAATCCCCCCCCAGCCAGTAACTTCTCTTTTTCTCGCCGCCCTGCGTCAGCgtg                             <  2:875236/76‑1 (MQ=255)
                                             cGGCCTTTTTATTTCACCACCTAATCCTCCACCAGCCAGTAACTTCTCTTTTTCTCGCCGCCCTGCGTCAGCgtgt                            >  1:1748966/1‑76 (MQ=255)
                                               gcttttttATTCCCCCCCCTACCCCCCCCCCAGCCAGTAACTTCTCTTTTTCTCGCCGCCCTGCGTCAGCGTGttt                          <  2:1826042/73‑1 (MQ=255)
                                               gCCTTTTTATTTCCCCCCCTAATCCCCCCCCAGCCAGTAACTTCTCTTTTTCTCGCCGCCCTGCGTCAGCGTGttt                          <  2:1826021/76‑1 (MQ=255)
                                               gCCTTTTTATTTCACCCCCTAACCCTCCCCCAGCCAGTAACTTCTCTTTTTCTCGCCGCCCTGCGTCAGCGTGttt                          <  1:311568/76‑1 (MQ=255)
                                               gCCTTTTTATTCCACCCCCTAACCCCCCCCCAGCCAGTAACTTCTCTTTTTCTCGCCGCCCTGCGTCAGCGTGttt                          <  2:1044685/76‑1 (MQ=255)
                                                 cTTTTTATTTCCCCCCCTAACCCTCCCCCAGCCAGTAACTTCTCTTTTTCTCGCCGCCCTGCGTCAGCGTGTTTAg                        <  2:821/76‑1 (MQ=255)
                                                  tttttATTTCACCACCTAATCCTCCACCAGCCAGTAACTTCTCTTTTTCTCGCCGCCCTGCGTTAGCGTGTTTAGc                       >  1:796771/1‑76 (MQ=255)
                                                   ttttATTTCACCCCCTACCCCTCCCCCAGCCAGTAACTTCTCTTTTTCTCGCCGCCCTGCGTCAGCGTGTTTAGcc                      <  2:741155/76‑1 (MQ=255)
                                                      tATTCCCCCCCCTACCCCCCCCCCAGCCAGTAACTTCTCTTTTTCTCGCCGCCCTGCGTCAGCGTGTTTAGCCACt                   <  1:451600/76‑1 (MQ=255)
                                                        tttCCCCCCCTAACCCCCCCCCAGCCAGTAACTTCTCTTTTTCTCGCCGCCCTGCGTCAGCGTGTTTAGCCACTGt                 <  1:1045977/76‑1 (MQ=255)
                                                         ttCCCCCCCCAACCCCCCCCCAGCCAGTAACTTCTCTTTTTCTCGCCGCCCTGCGTCAGCGTGTTTAGCCACTGTa                <  1:1933947/76‑1 (MQ=255)
                                                            cccaccCAACCCCCCCCCAGCCAGTAACTTCTCTTTTTCTCGCCGCCCTGCGTCAGCGTGTTTAGCCACTGTAACa             <  2:792117/75‑1 (MQ=255)
                                                            accaccTAATCCTCCACCAGCCAGTAACTTCTCTTTTTCTCGCCGCCCTGCGTCAGCGTGTTTAGCCACTGTAACa             >  1:1931838/1‑76 (MQ=255)
                                                              ccccTAACCCCCCCCCAGCCAGTAACTTCTCTTTTTCTCGCCGCCCTGCGTCAGCGTGTTTAGCCACTGTAACaaa           <  2:1956925/74‑1 (MQ=255)
                                                                  tAATCCTCCACCAGCCAGTAACTTCTCTTTTTCTCGCCGCCCTGCGTCAGCGTGTTTAGCCACTGTAACAAATAtt       >  1:383251/1‑76 (MQ=255)
                                                                   aaTCCTCCACCAGCCAGTAACTTCTCTTTTTCTCGCCGCCCTGCGTCAGCGTGTTTAGCCCCTGTAACAAATATTa      >  1:806396/1‑76 (MQ=255)
                                                                    aTCCTCCACCAGCCAGTAACTTCTCTTTTTCTCGCCGCCCTGCGTCAGCGTGTTTAGCCACTGTAACAAATATTaa     >  2:1071991/1‑76 (MQ=255)
                                                                       ctccACCAGCCAGTAACTTCTCTTTTTCTCGCCGCCCTGCGTCAGCGTGTTTAGCCACTGTAACAAATATTAAAAt  >  2:1267114/1‑76 (MQ=255)
                                                                           |                                                                       
TATCTGTGTAGAAATGCCCATTTAACTGCCTGAAGAGTAACCCAACGGCCTTTTTATTTCACCACCTAATCCTCCACCAGCCAGTAACTTCTCTTTTTCTCGCCGCCCTGCGTCAGCGTGTTTAGCCACTGTAACAAATATTAAAAT  >  REL606/2631697‑2631843

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑