Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,429,1640CG61.5% 6.6 / 11.6 13A39G (GCC→GGC) stfRputative prophage side tail fiber protein StfR
Reads supporting (aligned to +/- strand):  ref base C (3/2);  new base G (3/5);  total (6/7)
Fisher's exact test for biased strand distribution p-value = 5.92e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.08e-01
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

CGGTTTCATCGTGGGTGTCGGTTATAAGTTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGTTCAGGCGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCAGGTGTACTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACAATCCAGCTGAAAGCAAAACGTAACAGCACCACGGTGGTGGTGAACACGCTGGCCTCAGAAAATCCGGATGAAGCCGGGCGTTACAGCATGGACGTTGAGTACGGTCAGTACAGCGTTATTCTGTTGGTGGAAGGATTCCCGCCGTCACATGCCGGGACCATTACCGTGTATGAAGATTCTCAACCCGGTACGCTGAATGATTTTCTCGGTGCCATGACGGAGGATGATGCCCGTCCGGAGGCACTGCGCCGTTTTGAACTGATG  >  NC_000913/1428951‑1429375
                                                                                                                                                                                                                     |                                                                                                                                                                                                                   
cggattCATCGTTGGGGTCGGTTATAAATTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGAACCGGTGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCAGGAGTCCTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACCATTCAGCTGAAAGCCAGACGTAACAGCACCACGGTGGTGGTGAACACGGTGGGCTCAGAGAATCCGGATGAAGCCGGGCGTTACAGCATg                                                                                                                                                                                <  1:292511/247‑1 (MQ=255)
                                                                                                   tGGCAGTAAAGATTTCAGGAGTCCTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACCATTCAGCTGAAAGCCAGACGTAACAGCACCACGGTGGGGGTGAACACGGTGGGCTCAGAGAATCCGGATGAAGCCGGGCGTTACAGCATGTATGTGGAGTACGGTCAGTACAgtgtcatcctgcagg                                                                                                                                           <  1:85965/189‑15 (MQ=255)
                                                                                                    ngCAGTAAAGATTTCAGGTGTACTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACAATCCAGCTGAAAGCAAAACGTAACAGCACCACGGCGGAGGTGAACACGCTGGCCTCAGAAAATCCGGATGAAGCCGGGCGTTACAGCATGGACGTTGAGTACGGTCAGTACAGCGTTATTCTGTTGGTGGAAGGATTCCCGCCGTCACATGCCGGGACCATTACCGTGTATGAAGATTCTCAACCCGGt                                                                             >  1:37631/2‑250 (MQ=255)
                                                                                                       aGTAAAGATTTCAGGAGTCCTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACCATTCAGCTGAAAGCCAGACGTAACAGCACCACGGTGGTGGGGAACACGGTGGGCTCAGAGAATCTGGATTAAGCCGGGCGTTACAGCATGGATGTGGAGTACGGTCAGTACAgtgtcatcctgca                                                                                                                                             <  1:173338/183‑13 (MQ=255)
                                                                                                        gTAAAGATTTCAGGAGTCCTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACCATTCAGCTGAAAGCCAGACGGAACAGCACCACGGTGGTGGTGAACACGGTGGGCTCAGAGAATCCGGATGAAGCCGGGCGTTACAGCATGGATGTGGAGTACGGTCAGTACAGTGTCATCCTGCAGGTTGACGGTTTTCCACCATCGCACGCCGGGACCATCACCGTGTATGAAGATTCACAACCGGGGACGCt                                                                        <  1:3097/251‑1 (MQ=255)
                                                                                                                    ngagtccTGAAAGACGGCACATGAAAACCGGTACAGAACTGCACCATTCAGCTGAAAGCCAGACGTAACAGCACCACGGTGGTGGTGAACACGGTGGGCTCAGAGAATCCGGATGAAGCCGGGCGTTACAGCATGGATGTGGAGTACGGTCAGTACAGTGTCATCCTGCAGGTTGACGGTTTTCCACCATCGCACGCCGGGACCATCACCGTGTATGAAGATTCACAACCGGGGACGCTGAATGATTTtct                                                            >  1:81213/7‑251 (MQ=255)
                                                                                                                         ccTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACCATTCAGCTGAAAGCCAGACGTAACAGCACCACGGTGGTGGTGAACACGGTGGGCTCAGAGAATCCGGATGAAGCCGGGCGTTACAGCATGGATGTGGAGTACGGTCAGTACAGTGTCATCCTGCAGGTTGACGGTTTTCCACCATCGCACGCCGGGACCATCACCGTGTATGAAGATTCACAACCGGGGACGCTGAATGATTTTCTCtgtg                                                       >  1:70723/2‑251 (MQ=255)
                                                                                                                                  ctgCACAGGAAAACCGGTACAGAACTGCACAATCCAGCTGAAAGCAAAACGTAACAGCACCACGGTGGTGGTGAACCCGCTGGCCTCAGAAAATCCGGATGAAGCCGGGCGTTACAGCATGGACGTTGAGTACGGTCAGTACAGCGTTATTCTGTTGGTGGAAGGATTCCCGCCGTCACATGCCGGGACCATTACCGTGTATGAAGATTCTCAACCCGGTACGCTGAATGATTTTCTCGGTGCCATGACgg                                              >  1:315901/3‑251 (MQ=255)
                                                                                                                                       caGGAAAACCGGTACAGAACTGCACCATTCAGCTGAAAGCCAGACGTAACAGCACCACGGTGGTGGTGAACACGGTGGGCTCAGATAATCCGGATGAAGCCGGGCGTTACAGTATGGATGTGGAGTan                                                                                                                                                                    <  1:82020/128‑2 (MQ=255)
                                                                                                                                                          cTGCACAATCCAGCTGAAAGCAAAACGTAACAGCACCACGGTGGTGGTGAACACGCTGGCCTCAGAAAATACGGATGAAGCCGGGCGTTACAGCATGGACGTTGAGTACGGTCAGTACAGCGTTATTCTGTTGGTGGCAGGATTCCCGCCGTCACATGCCGGGACCATTACCGTGTATGAAGATTCTCAACCCGGTACGCTGAATGCTTTTCTCAGTGCCATGACGGAGGATGATGCCCGTCCGGAGGCAc                      >  1:313721/1‑251 (MQ=255)
                                                                                                                                                                        tGAAAGCCAGACGTAACAGCACCACGGTGGTGGTGAACACGGTGGGCTCAGAGAATCCGGATGAAGCCGGGCGTTACAGCATGGATGTGGAGTACGGTCAGTACAGTGTCATCCTGCAGGTTGACGGTTTTCCACCATCGCACGCCGGGACCATCACCGTGTATGAAGATTCACAACCGGGGACGCTGAATGATTTTCTCTGTGCCATGACGGAGgatg                                        >  1:119152/1‑219 (MQ=255)
                                                                                                                                                                              cAAAACGTAACAGCGCCACGGGGGTGGTGAACCCGCTGGCCTCAGAAAATCCGGAGGAAGCCGGGCGTTACAGCATGGACGTTGAGGACGGTCAGTACAGCGTTATTCTGTTGGTGGAAGGATTCCCGCCGTCACATGCCGGGACCATTACCGTGTATGAAGATTCTCAACCCGGTACGCTGAATGATTTTCTCGGTGCCATGACGGAGGATGATGCCCGTCCGGAGGCACTGCGCCGTTTTGAACTGAtg  <  1:297767/251‑1 (MQ=255)
                                                                                                                                                                                          tcaccacGGTGGTGGTGAACACGCTGGCCTCAGAAAATCCGGATGAAGCCGGGCGTTACAGCATGGACGTTGa                                                                                                                                                                        <  1:106863/72‑1 (MQ=255)
                                                                                                                                                                                                          gANCACNGNNGNNTCANAGAATCCGGATGAAGCCGGGCNNTACAGCATGNATGTGGAGTACGGTCAGTACAGTGTCATCCTGCAGGTTGACGGTTTTCCACCANCGCACGCCGNNACNATCACNGNNNANNNAGNTTCACAACCGGGGACGCTGNATNNTTTTCTNTGTGCCATGACGGAGGATGATGCCCg                                 <  2:70723/192‑1 (MQ=255)
                                                                                                                                                                                                                     |                                                                                                                                                                                                                   
CGGTTTCATCGTGGGTGTCGGTTATAAGTTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGTTCAGGCGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCAGGTGTACTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACAATCCAGCTGAAAGCAAAACGTAACAGCACCACGGTGGTGGTGAACACGCTGGCCTCAGAAAATCCGGATGAAGCCGGGCGTTACAGCATGGACGTTGAGTACGGTCAGTACAGCGTTATTCTGTTGGTGGAAGGATTCCCGCCGTCACATGCCGGGACCATTACCGTGTATGAAGATTCTCAACCCGGTACGCTGAATGATTTTCTCGGTGCCATGACGGAGGATGATGCCCGTCCGGAGGCACTGCGCCGTTTTGAACTGATG  >  NC_000913/1428951‑1429375

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑