Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,041,9400CA20.6% 81.6 / 15.2 34intergenic (+25/+90)appA/etkphosphoanhydride phosphorylase/tyrosine‑protein kinase, role in O‑antigen capsule formation
Reads supporting (aligned to +/- strand):  ref base C (12/15);  new base A (4/3);  total (16/18)
Fisher's exact test for biased strand distribution p-value = 6.81e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.80e-01
Rejected as consensus: Frequency below/above cutoff threshold.

GCCGCCCGGAGAGGTGAAACTGACCCTGGCAGGATGTGAAGAGCGAAATGCGCAGGGCATGTGTTCGTTGGCAGGTTTTACGCAAATCGTGAATGAAGCACGCATACCGGCGTGCAGTTTGTAATGCATAAAAAAGAGCATTCAGTTACCTGAATGCTCTGAGGCTGATGACAAACGAAGAACTGTCTAATGCGTAGACCGGAAAAGGCGTTCACGCCGCATCCGGCCACTTTCAGTTTTACTCTTTCTCGGAGTAACTATAACCGTAATAGTTATAGCCGTAA  >  NC_000913/1041792‑1042075
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gccgccTGGAGAGGTGAAACTGACCCTGGCAGGATGTGAAGAGCGAAATGCGCAGGGCATGTGTTCGTTGGCAGGTTTTACGCAAATCGTGAATGAAGCACGCATACCGGCGTGCAGTTTGTAATGCATAAAAAAGAGCATTCAGTTAc                                                                                                                                         <  1:58689/149‑1 (MQ=255)
gccgccCGGAGAGGTGAAACTGACCCTGGCAGGATGTGAAGAGCGAAATGCGCAGGGCATGTGTTCGTTGGCAGGTTTTACGCAAATCGTGAATGAAGCACGCATACCGGCGTGCAGTTTGTAATGCATAAAAAAGAGCATTCAGTTAc                                                                                                                                         >  5:170895/1‑149 (MQ=255)
  cgccCGGAGAGGTGAAACTGACCCTGGCAGGATGTGAAGAGCGAAATGCGCAGGGCATGTGTTCGTTGGCAGGTTTTACGCAAATCGTGAATGAAGCACGCATACCGGCGTGCAGTTTGTAATGCATAAAAAAGAGCATTCAGTTACCt                                                                                                                                       <  6:170895/149‑1 (MQ=255)
                   cTGACCCTGGCAGGATGTGAAGAGCGAAATGCGCAGGGCATGTGTTCGTTGGCAGGTTTTACGCAAATCGTGAATGAAGCACGCATACCGGCGTGCAGTTTGTAATGCATAAAAAAGAGCATTCAGTTACCTGAATGCTCTGAGGCtga                                                                                                                      <  1:49355/149‑1 (MQ=255)
                              aGGATGTGTAGAGCGAAATGCGCAGGGCATGTGTTCGTTGGCAGGTTTTACGCAAATCGTGAATGAAGCACGCATACCGGCGTGCAGTTTGTAATGCATAAAAAAGAGCATTCAGTTACCTGAATGCTCTGAGGCTGATGACAAACg                                                                                                             >  6:45075/1‑147 (MQ=255)
                                    tgAAGAGCGAAATGCGCAGGGCATGTGTTCGTTGGCAGGTTTTACGCAAATCGTGAATGAAGCACGCATACCGGCGTGCAGTTTGTAATGCATAAAAAAGAGCATTCAGTTACCTGAATGCTCTGAGGCTGATGACAAACGAAGAACt                                                                                                      <  6:119530/148‑1 (MQ=255)
                                        gagCGAAATGCGCAGGGCATGTGTTCGTTGGCAGGTTTTACGCAAATCGTGAATGAAGCACGCATACCGGCGTGCAGTTTGTAATGCATAAAAAAGAGCATTCAGTTACCTGAATGCTCTGAGGCTGATGACAAACGAAGAACTGTCt                                                                                                  >  2:143863/1‑148 (MQ=255)
                                        gagCGAAATGCGCAGGGCATGTGTTCGTTGGCAGGTTTTACGCAAATCGTGAATGAAGCACGCATACCGGCGTGCAGTTTGTAATGCATAAAAAAGAGCATTCAGTTACCTGAATGCTCTGAGGCTGATGACAAACGAAGAACTGTCt                                                                                                  >  2:158653/1‑148 (MQ=255)
                                                          aTGTGTTCGTTGGCAGGTTTTACGCAAATCGTGAATGAAGCACGCATACCGGCGTGCAGTTTGTAATGCATAAAAAAGAGCATTCAGTTACCTGAATGCTCTGAGGCTGATGACAAACGAAGAACTGTCTAATGCGTAGACCGGAAAAg                                                                               <  1:143863/149‑1 (MQ=255)
                                                          aTGTGTTCGTTGGCAGGTTTTACGCAAATCGTGAATGAAGCACGCATACCGGCGTGCAGTTTGTAATGCATAAAAAAGAGCATTCAGTTACCTGAATGCTCTGAGGCTGATGACAAACGAAGAACTGTCTAATGCGTAGACCGGAAAAg                                                                               <  1:158653/149‑1 (MQ=255)
                                                             tgtTCGTTGGCAGGTTTTACGCAAATCGTGAATGAAGCACGCATACCGGCGTGCAGTTTGTAATGCATAAAAAAGAGCATTCAGTTACCTGAATGCTCAGAGGCTGATGACAAACGAAGAACTGTCTAATGCGTAGACCGGAAAAGGCg                                                                            >  6:3146/1‑149 (MQ=255)
                                                                  gTTGGCAGGTTTTACGCAAATCGTGAATGAAGCACGCATACCGGCGTGCAGTTTGTAATGCATAAAAAAGAGCATTCAGTTACCTGAATGCTCTGAGGCTGATGACAAACgaagaa                                                                                                        <  8:99683/116‑1 (MQ=255)
                                                                  gTTGGCAGGTTTTACGCAAATCGTGAATGAAGCACGCATACCGGCGTGCAGTTTGTAATGCATAAAAAAGAGCATTCAGTTACCTGAATGCTCTGAGGCTGATGACAAACgaagaa                                                                                                        >  7:99683/1‑116 (MQ=255)
                                                                  gTTGGCAGGTTTTACGCAAATCGTGAATGAAGCACGCATACCGGCGTGCAGTTTGTAATGCATAAAAAAGAGCATTCAGTTACCTGAATGCTCTGAGGCTGATGACAAACGAAGAACTGTc                                                                                                   >  1:183891/1‑121 (MQ=255)
                                                                  gTTGGCAGGTTTTACGCAAATCGTGAATGAAGCACGCATACCGGCGTGCAGTTTGTAATGCATAAAAAAGAGCATTCAGTTACCTGAATGCTCTGAGGCTGATGACAAACGAAGAACTGTc                                                                                                   <  2:183891/121‑1 (MQ=255)
                                                                  gTTGGCAGGTTTTACGCAAATCGTGAATGAAGCACGCATACCGGCGTGCAGTTTGTAATGCATAAAAAAGAGCATTCAGTTACCTGAATGCTCTGAGGCTGATGACAAACGAAGAACTGTCTAATGCGTa                                                                                          >  4:36028/1‑130 (MQ=255)
                                                                       cAGGTTTTACGCAAATCGTGAATGAAGCACGCATACCGGCGTGCAGTTTGTAATGCATAAAAAAGAGCATTCAGTTACCTGAATGCTCTGAGGCTGATGACAAAc                                                                                                              <  5:6668/105‑1 (MQ=255)
                                                                       cAGGTTTTACGCAAATCGTGAATGAAGCACGCATACCGGCGTGCAGTTTGTAATGCATAAAAAAGAGCATTCAGTTACCTGAATGCTCTGAGGCTGATGACAAAc                                                                                                              >  6:6668/1‑105 (MQ=255)
                                                                                                aGCACGCATACCGGCGTGCAGTTTGTAATGCATAAAAAAGAGCATTCAGTTACCTGAATGCTCAGAGGCTGATGACAAACGAAGAACTGTCTAATGCGTAGACCGGAAAAGGCGTTCACGCCGCATCCGGCCACTTTCAGTTTTActct                                         <  5:3146/149‑1 (MQ=255)
                                                                                                     gCATACCGGCGTGCAGTTTGTAATGCATAAAAAAGAGCATTCAGTTACCTGAATGCTCTGAGGCTGATGACAAACGAAGAACTGTCTAATGCGTAGACCGGAAAAGGCGTTCACGCCGCATCCGGCCACTTTCAGTTTTACTCTTtctc                                    <  5:45075/149‑1 (MQ=255)
                                                                                                      cATACCGGCGTGCAGTTTGTAATGCATAAAAAAGAGCATTCAGTTACCTGAATGCTCTGAGGCTGATGACAAACGAAGAACTGTCTAATGCGTAGACCGGAAAAGGCGTTCACGCCGCATCCGGCCACTTTCAGTTTTACTCTTTCTCg                                   <  6:127864/149‑1 (MQ=255)
                                                                                                                     tttGTAATGCATAAAAAAGAGCATTCAGTTACCTGAATGCTCTGAGGCTGATGACAAACGAAGAACTGTCTAATGCGTAGACCGGAAAAGGCGTTCACGCCGCATCCGGCCACTTTCAGTTTTACTCTTTCTCGGAGTAACTATAACCg                    >  7:76206/1‑149 (MQ=255)
                                                                                                                          aaTGCATAAAAAAGAGCATTCAGTTACCTGAATGCTCTGAGGCTGATGACAAACgaa                                                                                                           <  4:14368/57‑1 (MQ=255)
                                                                                                                          aaTGCATAAAAAAGAGCATTCAGTTACCTGAATGCTCTGAGGCTGATGACAAACgaa                                                                                                           >  3:14368/1‑57 (MQ=255)
                                                                                                                                 aaaaaaGAGCATTCAGTTACCTGAATGCTCTGAGGCTGATGACAAACGAAGAACTGTCTAATGCGTAGACCGGAAAAGGCGTTCACGCCGCATCCGGCCACTTTCAGTTTTACTCTTTCTCGGAGTAACTATAACCGTAATAGTTATAg        >  5:144996/1‑149 (MQ=255)
                                                                                                                                  aaaaaGAGCATTCAGTTACCTGAATGCTCTGAGGCTGATGACAAACGAAGAACTGTCTAATGCGTAGACCGGAAAAGGCGTTCACGCCGCATCCGGCCACTTTCAGTTTTACTCTTTCTCGGAGTAACTATAACCGTAATAGTTATAg        <  8:76206/148‑1 (MQ=255)
                                                                                                                                    tcagagCATTCAGGTAACTGAATGCTCTGAGGCTGATGACAAACGAAGAACTGTCTAATGCGTAGACCGGAAAAGGCGTTCAc                                                                       <  7:20621/81‑1 (MQ=255)
                                                                                                                                    tcagagCATTCAGGTAACTGAATGCTCTGAGGCTGATGACAAACGAAGAACTGTCTAATGCGTAGACCGGAAAAGGCGTTCAc                                                                       >  8:20621/3‑83 (MQ=255)
                                                                                                                                     cagagCATTCAGGTAACTGAATGCTCTGAGGCTGATGACAAACGAAGAACTGTCTAATGCGTAGACCGGAAAAGGCGTTCACGCCGCATCCGGCCACTTTCAGTTTTa                                             >  3:80080/2‑108 (MQ=255)
                                                                                                                                     cagagCATTCAGGTAACTGAATGCTCTGAGGCTGATGACAAACGAAGAACTGTCTAATGCGTAGACCGGAAAAGGCGTTCACGCCGCATCCGGCCACTTTCAGTTTTa                                             <  4:80080/107‑1 (MQ=255)
                                                                                                                                     cagagCATTCAGGTAACTGAATGCTCTGAGGCTGATGACAAACGAAGAACTGTCTAATGCGTAGACCGGAAAAGGCGTTCACGCCGCATCCGGCCACTTTCAGTTTTACTCTTTCTCGGAGTAACTATAACCGTAATAGTTATAg        >  6:62876/2‑145 (MQ=255)
                                                                                                                                     cagagCATTCAGGTAACTGAATGCTCTGAGGCTGATGACAAACGAAGAACTGTCTAATGCGTAGACCGGAAAAGGCGTTCACGCCGCATCCGGCCACTTTCAGTTTTACTCTTTCTCGGAGTAACTATAACCGTAATAGTTATAg        <  5:62876/144‑1 (MQ=255)
                                                                                                                                       gagCTTTCAGTTACCTGAAGGCTCTGAGGCTGATGACAAACGAAGAACTGTCTAATGCGTAGACCGGAAAAGGCGTGCACGCCGCATCCGGCCACTTTCAGTTTTACTCTTTCTCGGAGTAACTATAACCGTAATAGTTATAGCCGTaa  <  6:125769/149‑1 (MQ=255)
                                                                                                                                       gagCATTCAGGTAACTGAATGCTCTGAGGCTGATGACAAACGAAGAACTGTCTAATGCGTAGACCGGAAAAGGCGTTCACGCCGCATCCGGCCACTTTCAGTTTTACTCTTTCTCGGAGTAACTATAACCGTAATAGTTATAGCCGTaa  >  1:13978/1‑149 (MQ=255)
                                                                                                                                               aGTTACCTGAATGCTCTGAGGCTGATGACAAACGAAGAACTGTCTAATGCGTAGACCGGAAAAGGCGTTCACGCCGCATCCGGCCACTTTCAGTTTTa                                             <  7:14298/98‑1 (MQ=255)
                                                                                                                                               aGTTACCTGAATGCTCTGAGGCTGATGACAAACGAAGAACTGTCTAATGCGTAGACCGGAAAAGGCGTTCACGCCGCATCCGGCCACTTTCAGTTTTa                                             >  8:14298/1‑98 (MQ=255)
                                                                                                                                                    |                                                                                                                                       
GCCGCCCGGAGAGGTGAAACTGACCCTGGCAGGATGTGAAGAGCGAAATGCGCAGGGCATGTGTTCGTTGGCAGGTTTTACGCAAATCGTGAATGAAGCACGCATACCGGCGTGCAGTTTGTAATGCATAAAAAAGAGCATTCAGTTACCTGAATGCTCTGAGGCTGATGACAAACGAAGAACTGTCTAATGCGTAGACCGGAAAAGGCGTTCACGCCGCATCCGGCCACTTTCAGTTTTACTCTTTCTCGGAGTAACTATAACCGTAATAGTTATAGCCGTAA  >  NC_000913/1041792‑1042075

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑