Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,001,9180AC45.5% 26.2 / 19.9 33intergenic (‑129/+192)fliA/fliCRNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein
Reads supporting (aligned to +/- strand):  ref base A (17/1);  new base C (0/15);  total (17/16)
Fisher's exact test for biased strand distribution p-value = 1.54e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

AATTCACGATAAACAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATAAGCGCAGC  >  NC_000913/2001783‑2002057
                                                                                                                                       |                                                                                                                                           
aaTTCACGATAAACAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAAcccc                                                                                                                                         >  1:489908/1‑140 (MQ=255)
 aTTCACGATAAACAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCccg                                                                                                                                        >  1:114649/1‑140 (MQ=255)
      cGATAAACAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGt                                                                                                                                   >  1:9453/1‑140 (MQ=255)
                cccTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAg                                                                                                                         >  1:659685/1‑140 (MQ=255)
                    gctttATATGAGTTATCGGCATGATTATCCGTTTCTGCGGGTTTTTTAATCGGACGATTAGTGGGTAAAATGGGGGTTTATTGGGGGGTTACAGGTAAATCCCAGGAAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACg                                                                                                                     <  1:83886/137‑1 (MQ=255)
                      gTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGtt                                                                                                                   >  1:730481/1‑140 (MQ=255)
                               gTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACaaa                                                                                                          >  2:155212/1‑140 (MQ=255)
                               gTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACaaa                                                                                                          >  1:413935/1‑140 (MQ=255)
                               gTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACaaa                                                                                                          >  1:445714/1‑140 (MQ=255)
                                  aTCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTg                                                                                                       >  1:303417/1‑140 (MQ=255)
                                    gggCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGTTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTgcg                                                                                                     <  1:210665/139‑1 (MQ=255)
                                    cGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTgcg                                                                                                     >  2:445220/1‑140 (MQ=255)
                                    cGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAAGGGGGGGTTATTGGGGGGTTACAGGTAAATTCCAGGCAGAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTgcg                                                                                                     <  1:243596/140‑1 (MQ=255)
                                                      cTGCAGGGTTTTTAATCGGACGATTAGGGGGTAAAATGAGGGTTTATTTGGGGGTTACAGGAAAATTCCAGGCAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATgc                                                                                   <  2:23686/140‑1 (MQ=255)
                                                        gcgggttttttAATCGGACGATTAGTGGGTAAAATGGGGGTTTTTTGGGGGGTTACAGGTAAATTCCAGGCAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATgcgg                                                                                 <  2:730481/134‑1 (MQ=255)
                                                                        gACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATcc                                                                 >  1:772615/1‑140 (MQ=255)
                                                                        gACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATcc                                                                 >  1:128688/1‑140 (MQ=255)
                                                                        gACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATcc                                                                 >  1:261566/1‑140 (MQ=255)
                                                                         aCGATTAGTGGGTGAAATGGGGGTTTATTTGGGGGTTAAAGGTAAATCCCGGGAAGAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCg                                                                <  2:244831/140‑1 (MQ=38)
                                                                                     tGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAAt                                                    >  1:640745/1‑140 (MQ=255)
                                                                                         aTGAGGGGTTATTGGGGGTTTACAGGTAAATTCCAGGAAGAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGc                                                <  1:341632/140‑1 (MQ=255)
                                                                                                      ggggggTTAAAGGTAAATCCCAGGCAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAAt                                   <  2:261566/139‑1 (MQ=255)
                                                                                                       gggggTTACAGGTAAATTCCAGGAAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAAtt                                  <  1:155212/140‑1 (MQ=255)
                                                                                                       gggggTTAAAGGAAAATTCCAGGAAAAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAAtt                                  <  2:303417/140‑1 (MQ=255)
                                                                                                             tACAGGTAAATCCCAGGAAGAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAAtt                            <  2:688456/140‑1 (MQ=255)
                                                                                                              aCAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTc                           >  2:494925/1‑140 (MQ=255)
                                                                                                               cAGGTAAATCCCAGGCAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCa                          <  2:85837/140‑1 (MQ=255)
                                                                                                               aggcaaaaTTCGAGGAAGAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCa                          <  2:103236/135‑1 (MQ=37)
                                                                                                               aaGGTAAATTCCAGGAAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCa                          <  2:9453/139‑1 (MQ=255)
                                                                                                                    aaaTTCCAGGCAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTg                     <  1:407974/140‑1 (MQ=255)
                                                                                                                    aaaTTCCAGGCAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTg                     <  1:418345/140‑1 (MQ=255)
                                                                                                                     aaTTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGt                    >  2:167239/1‑140 (MQ=255)
                                                                                                                            ggCAGAAAAAAACCCCGCCGGGGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTATAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTg             >  1:149934/1‑140 (MQ=255)
                                                                                                                                       aCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATAagcgcagc  >  2:463768/1‑140 (MQ=255)
                                                                                                                                       |                                                                                                                                           
AATTCACGATAAACAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATAAGCGCAGC  >  NC_000913/2001783‑2002057

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑