Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,001,9110GA44.0% 19.2 / 11.6 25intergenic (‑122/+1)fliA/fliXRNA polymerase sigma factor FliA/small RNA FliX
Reads supporting (aligned to +/- strand):  ref base G (12/2);  new base A (0/11);  total (12/13)
Fisher's exact test for biased strand distribution p-value = 2.02e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

CTGCAGGCGCAATGCTTCGTGACGCACCAGCGGGACATAACGCTGCCACAGCGAGTGTTT‑ATCCATTACACCTTCAGCGGTATAGAGTGAATTCACGATAAACAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAA‑TCGGACGATTAGTGGGTGAAATGAGGGGTT‑ATTTGGGGG‑TT‑ACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATAAGCGCAGCGCATCAGGCAATTTGGCGTTGCCGTCAGTCTCAGTTAATCAGGTTACAACGATTAACCCTGCAGCAGAGACAGAACCTGCTGCGGTACCTGGTTAGCT  >  NC_000913/2001694‑2002155
                                                                                                                                                                                                                              |                                                                                                                                                                                                                                                    
cggCAGGCCCAATGCTTGGTGCCGCCCCGGGGGGACAAAACGCGGCCACAGGGGGTTTTT‑ATCCATTACACCTGAGGGGGTATAGAGTAAATTCACGAAAAACAGCCTTGCTTTATATGATTTATCGGAATGATTATCCGTTTCTGCGGGGTTTTTAC‑TCGGACGATTGGGGGGAAAAAGGAGGGTTT‑TTTTGGGGG‑TG‑ACAGGTAAATTCCGGAAAAAAAAAAACCCCGCCGGTGGCGGGGAAGCACGtt                                                                                                                                                                                                                     <  2:165683/249‑1 (MQ=255)
                  gtgccGCACCAGCGGGACATAACGCTGCCACAGCGAGTTTTT‑ACCCATTCCCCCTTCAGCGGTATAGAGTGAATTCACGAAAAACAGCCCTGCTTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAA‑TCGGACGATTAGGGGGTAAAATGAGGGGTT‑ATTTGGGGG‑TT‑ACAGGTAAATTCCAGGCAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCttt                                                                                                                                                                                                   <  1:170036/247‑1 (MQ=255)
                    gACGCACCAGCGGGACATAACGCTGCCACAGCGAGTGTTT‑ATCCATTACACCTTCAGCGGTATAGAGTGAATTCACGATAAACAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAA‑TCGGACGATTAGTGGGTGAAATGAGGGGTT‑ATTTGGGGG‑TT‑ACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTAt                                                                                                                                                                                                 >  1:98700/1‑251 (MQ=255)
                                  aCATAACGCTGCCACAGCGAGTGTTC‑ATCCATTCCACCTTCAGCGGTATAGAGTGAATTCACGATAAACAGCCCTGCGTTATATGAGTTATCGGCATGATTATACGTTTCTGCAGGGTTTTTAA‑TCGGACGATTATAGGGTGAAATGAGGGGTT‑ATTTGGGGG‑TT‑ACAGGTAAATTCCAGGCAGAAAAAAAGCCCGCCGGTAGCGGGGAAGCACGTTGATCACAAATTGAGCTTTATGTTGCCAGATacgg                                                                                                                                                                                   >  2:349413/1‑251 (MQ=255)
                                     aaaCGCGGCCAAAGCGAGTTTTT‑ATCCATTCCACCTTCAGCGGTATAGAGTGAATTCACGATAAACGCCCCTGCTTTATAGGAGTTATGGGAATGATTAGCCGTTTCGGCAGGGTTTTAAA‑GCGGACGATTGGTGGGTAAAAGGAGGGTTT‑ATTGGGGGG‑TT‑AAAGGTAAATCCCAGGCAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGt                                                                                                                                                                                <  1:199777/250‑1 (MQ=255)
                                         gCTGCCACAG‑GAATGTTTTACCCATTACCCCTTGAGGGGTAGAGAGTAAATTCACGAAAAACGGCCCGGCTTTATATGATTTATCGGCAGGATTATCCTTTTCTGCAGGTTTTTTAA‑TGGGACG‑TTGGGGGGGGAAAAGGGGGGTTTATTGGGGGT‑TT‑ACAGGTAAATCCCAGGCAGAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTGGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAAc                                                                                                                                                                            <  1:232694/251‑1 (MQ=255)
                                                          ccacacgaccctcgccagatttgTATAGAGTAAATTCACGATAAACAGCCCTGTTTTATATGAGTTATCGGAATGATTATCTGTTTCTG‑GGGGTTTTTAAATCGGAGGATGAGGGGGAAAAATGAGGTGTT‑ATTTGGGGG‑TG‑ACAGAAAAATTCCAGGAAAAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTAc                                                                                                                                                            <  2:78183/229‑1 (MQ=255)
                                                                               ggTATAGAGTGAATTAACGATAAACAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAA‑TCGGACGATTAGTGGGTGAAATGAGGGGTT‑ATTTGGGGG‑TT‑ACAGGTAAATTCCAGGCAGCAAAAAACCCCGCCGGTGGCGGGGAAGCCCGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATa                                                                                                                                        >  1:120987/1‑250 (MQ=255)
                                                                                gTATAGAGTGAATTCACGATAAACAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAA‑TCGGACGATTAGTGGGTGAAATGAGGTGTT‑ATTTGGGGG‑TT‑ACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTAc                                                                                                                                                            >  1:78183/1‑229 (MQ=255)
                                                                                       gTGAATTCACGAAAAACAGCCCTGTTTTATATGAGTTATGGGAATGATTATCCGTTTCTGCAGGTTTTTTAA‑TCGGACGATTAGGGGGTGAAATGAGGG‑TT‑TTTTGGGGG‑TTTACAGGTAAATTCCAGGAAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAAt                                                                                                                               <  1:91557/251‑1 (MQ=255)
                                                                                                          cccTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAA‑TCGGACGATTAGTGGGTGAAATGAGGGGTT‑ATTTGGGGG‑TT‑ACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGAt                                                                                                             >  1:293627/1‑250 (MQ=255)
                                                                                                                 ttATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAA‑TCGGACGATTAGTGGGTGAAATGAGGGGTT‑ATTTGGGGG‑TT‑ACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAACCGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATAagcgc                                                                                                       >  1:57795/1‑249 (MQ=255)
                                                                                                                                gctttatttcccGTTTCTGCAGGTTTTTTAA‑TCGGCCGATTGGTGGGTGAAAGGAGGGTTT‑ATTTGGGGT‑TT‑ACAGATAAATCCCAGGCAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATAAGCGCAGCGCATCAGGCAAttt                                                                                      <  1:283609/241‑1 (MQ=37)
                                                                                                                                     aTTATCCGTTTCTGCAGGGTTTTTAA‑TCGGACGATTAGTGGGTGAAATGAGGGGTT‑ATTTGGGGG‑TT‑ACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATAAGCGCAGCGCATCAGGCAATTTGGCGt                                                                                 >  1:64398/1‑251 (MQ=255)
                                                                                                                                       tATCCGTTTCTGCAGGGTTTTTAA‑TCGGACGATTAGTGGGTGAAATGAGGGGTT‑ATTTGGGGG‑TT‑ACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATAAGCGCAGCGCATCAGGCAATTTGGCGTTg                                                                               >  2:214622/1‑251 (MQ=255)
                                                                                                                                                           ttAA‑TCGGACGATTAGTGGGTGAAATGAGGGGTT‑ATTTGGGGG‑TT‑ACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATAAGCGCAGCGCATCAGGCAATTTGGCGTTGCCGTCAGTCTCAGTTAATc                                                            >  1:261795/1‑250 (MQ=255)
                                                                                                                                                            tAA‑TCGGACGATTAGTGGGTGAAATGAGGGGTT‑ATTTGGGGG‑TT‑ACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACaaaaa                                                                                                                                                       >  1:281069/1‑158 (MQ=255)
                                                                                                                                                                   agggATTAGTGGGAAAAATGGGGGTTT‑TTTTGGGGG‑TA‑AGAGATAAATCCAAGGAAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATAAGCGCAGCGCATCAGGCAATTTGGCGTTGCCGTCAGTCTCAGTTAATCAGGTTACa                                                    <  2:221740/248‑1 (MQ=37)
                                                                                                                                                                         tatggggTGAAAGGAGGG‑TT‑ATTTGGGGGGTT‑ACAGGAAAATTCCAGGCAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATAAGCGCAGCGCATCAGGCAATTTGGCGTTGCCGTCAGTCTCAGTTAATCAGGTTACAACGAt                                               <  1:312117/246‑1 (MQ=38)
                                                                                                                                                                         tagggggTGAAATGGGGTGTT‑ATTTGGGGG‑TT‑ACAGGTAAATCCCAGGAAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATAAGCGCAGCGCATCAGGCAATTTGGCGTTGCCGTCAGTCTCAGTTAATCAGGTTACAACGAt                                               <  1:312115/246‑1 (MQ=255)
                                                                                                                                                                           gggggTGAATTGGGGGGTT‑TTTTGGGGG‑TT‑ACAGGTAAATCCCAGGCAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATAAGCGCAGCGCATCAGGCAATTTGGCGTTGCCGTCAGTCTCAGTTAATCAGGTTACAACGATTaa                                            <  2:14903/249‑1 (MQ=38)
                                                                                                                                                                                     tGAGGGGTT‑ATTTGGGGG‑TT‑ACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATAAGCGCAGCGCATCAGGCAATTTGGCGTTGCCGTCAGTCTCAGTTAATCAGGTTACAACGATTAACCCTgcagc                                   >  1:296294/1‑250 (MQ=255)
                                                                                                                                                                                               aTTTGGGGG‑TT‑ACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATAAGCGCAGCGCATCAGGCAATTTGGCGTTGCCGTCAGTCTCAGTTAATCAGGTTACAACGATTAACCCTGCAGCAGAGACAGa                          >  1:12614/1‑250 (MQ=255)
                                                                                                                                                                                                                 aaaaTACCAGACAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTGTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGTCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACGTGTAGGCCTGATAAGCGCAGCGCATCAGGCAATTTGGCGTGGCCGTCAGTCTCAGTTAATCAGGTTACAACGTTTAACCCTGCAGCAGAGACAGAACCTGCTGCTGTACCTg         <  1:17295/250‑1 (MQ=38)
                                                                                                                                                                                                                        atggCAAAAAAAACCCCCGCCGTTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGTATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTGTTAGGCCTGATAAGCTCAGCGCAGCAGGCAATTTGGCGTTGCCGTCAGTCTCAGTTAATCAGGTGACAACGATTAACCCTGCAGCAGAGACAGAACCTGCTGCGGTACCTGGTTAGCt  <  1:274108/249‑1 (MQ=255)
                                                                                                                                                                                                                              |                                                                                                                                                                                                                                                    
CTGCAGGCGCAATGCTTCGTGACGCACCAGCGGGACATAACGCTGCCACAGCGAGTGTTT‑ATCCATTACACCTTCAGCGGTATAGAGTGAATTCACGATAAACAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAA‑TCGGACGATTAGTGGGTGAAATGAGGGGTT‑ATTTGGGGG‑TT‑ACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATAAGCGCAGCGCATCAGGCAATTTGGCGTTGCCGTCAGTCTCAGTTAATCAGGTTACAACGATTAACCCTGCAGCAGAGACAGAACCTGCTGCGGTACCTGGTTAGCT  >  NC_000913/2001694‑2002155

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑