Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913566,2050TC55.6% 7.0 / 26.0 28intergenic (‑227/‑479)intD/renDputative integrase/protein RenD
Reads supporting (aligned to +/- strand):  ref base T (6/6);  new base C (7/8);  total (13/15)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.67e-01
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

GAGACTGAAGCGCCGCAATGCAGGCTTGCCGTGTTGTGAGGTACCCGGATATTATCGTGAGGATGCGTCATCGCCATTGCTCCCCAAATACAAAACCAATTTCAGCCAGTGCCTCGTCCATTTTTTCGATGAACTCCGGCACCATCTCGTCAAAACTCGCCATGTACTTTTCATTCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGAGGTACGAGTATTGCCGGAAGCGTGGCCTGTATCCGGATGCAGAGTCTTATCCGTGGAAATCGAACGCGCATTACTGGTTGG  >  NC_000913/566031‑566454
                                                                                                                                                                              |                                                                                                                                                                                                                                                         
gagaCTGAAGCGCCGCAATGCAGGCTTGCCGTGTTGTGAGGTACCCGGATATTATCGTGAGGATGCGTCCTCGCCATTGCTCCCCAAATACAAAACCAATTTCAGCCAGTGCCTCGTCCATTTTTTCGATGAACTCCGGCACCATCTCGTCAAAACTCGCCATGTACTTTTCATTCCGCTCAATCAc                                                                                                                                                                                                                                               >  1:215794/1‑187 (MQ=255)
               cAATGCAGGCTTGCCGTGTTGTGAGGTACCCGGATATTATCGTGAGGATGCGCCATCGACCTTGCTCCCCAAATCCAAAACCAATTTCAGCCAGTGCCTCGTCCATTTTTTCGATGAACTCCGGCACCATATCGTCAAAACTCGCCATGTACTTTTCCTTCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATg                                                                                                                                                                >  1:164914/1‑251 (MQ=255)
                      agacgaaagtgattgcgcctACCCGGATATTATCGTGAGGATGCATCATCGCCAGTGCTCCCCAAATACAAAACCAATTTCAGCCAGTGCCTCGTCCATTTTTTCGATTATCGCCGGCACGATCTCGTCAAAACTCGCCATGTACTTTTCATCCCGCTCAAGCACGACAGGATGCAGATCGGCACGCTTCATGCGCGTGTCATAGTTGGCAAAGTACCAGGCATTTTTTCTCGTCACCCACATGCTGTAc                                                                                                                                                          <  1:184873/231‑1 (MQ=255)
                                  ttgcgcctACCCGGATATTATCGTGAGGATGCGTCATCGCCATTGCTCCCCAAATACAAAACCAATTTCAGCCAGTGCCTCGTCCTTTTTTTCGATGAACTCCGGCACGATCTCGTCAAAACTCGCCATGTACTTTTCATCCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGc                                                                                                                                                                                      <  1:232903/203‑1 (MQ=255)
                                       cctACCCGGATATTATCGTGAGGATGCGTCATCGCCATTGCTCCCCAAATACAAAACCAATTTCAGCCAGTGCCTCGTCCATTTTTTCGATGAACTCCGGCACGATCTCGTCAAAACTCGCCATGTACTTTTCNTCCNNNNNaannnnnn                                                                                                                                                                                                                                             >  2:193917/3‑144 (MQ=255)
                                       cctACCCGGATATTATCGTGAGGATGCGTCATCGCCATTGCTCCCCAAATACAAAACCAATTTCAGCCAGTGCCTCGTCCATTTTTTCGATGAACTCCGGCACGATCTCGTCAAAACTCGCCATGTACTTTTCATCCCGCTCAATCACGACATAATGCAGGCCttn                                                                                                                                                                                                                             <  1:193917/164‑2 (MQ=255)
                                           cccGGATATTATCGTGAGGATGCGTCATCGCCATTGCTCCCCAAATACAAAAACAATTTCAGACAGTGCCTCGTCCATTTTTTCGATGAACTCCGGCACCCTCTCGTCAAAACTCGCCATGTACTTTTCATTCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCCTAGTTGGCAACGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCAATGTAAGCCg                                                                                                                                    >  1:53994/1‑251 (MQ=255)
                                           cccGGATATTATCGTGAGGATGCGTCATCGCCATTGCCCCCCAAATACAAAACCAATGTCAGCCAGTGCCGCGTCCATTGTTGCGATGAACTCCGGCACCATCTCGGCAAAACTCGCCATGTACTTTGCATTCCGCTCAATCACGACATAATGCAGGCCGTCACGCTTCATGCGCgg                                                                                                                                                                                                              <  1:289156/177‑1 (MQ=255)
                                              ggATATTATCGTGAGGATGCGTCATCGCCATTGCTCCATAAATACAAAACCAATTTCAGCCAGTACCTCGTCCATTTTTTCGATGCACTACGGCACGCTCTCGTCAAAAATCGCCATGTACTTTTCATCCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTACTGCAACTGGGCAATGTAAGctgact                                                                                                                                 >  1:238775/1‑246 (MQ=255)
                                                            ggATGCGTCATCGCCATTGCTCCCCAAATACAAAACCAATTTCAGCCAGTGCCTCGTCCATTTTTTCGATGAACTCCGGCACCATCTCGTCAAAACTCGCCATGTACTTGTCATTCCGCTCAATCACGACATAATGCAGGCCTTCAc                                                                                                                                                                                                                           <  1:153237/147‑1 (MQ=255)
                                                             gATGCGTCATCGCCATTGCTCCCCAAATACAAAACCAATTTCAGCCAGTGCCTCGTCCATTTTTTCGATGAACTCCGGCACGATCTCGTCAAAACTCGCCATGTACTTTTCATCCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCTGACTTTATGGCCTCGAAac                                                                                                                  <  1:127071/251‑1 (MQ=255)
                                                                                  cccAAATACAAAACCAATTTCAGCCAGTGCCTCGTCCATTTTTTCGATGAACTCCGGCACGATCTCGTCAAAACTCGCCATGTACTTTTCATCCCGCTCAATCACGACATAATGCAGGCCTTCACGCtt                                                                                                                                                                                                                       >  1:77060/1‑129 (MQ=255)
                                                                                  cccAAATACAAAACCAATTTCAGCCAGTGCCTCGTCCATTNTTTCGATGANNTCNGGCACNANNNCNNNAANACTCGCCATGTACTTTTCANCCNNCTCAATNACGACATAATGCAGGCCTTCACGCtt                                                                                                                                                                                                                       <  2:77060/129‑1 (MQ=255)
                                                                                   ncAAATACAAAACCAATTTCAGCCAGTGCCTCGTCCATTTTTTCGATGAACTCCGGCACGATCTCGTCAAAACTCGCCATGTACTTTTCATCCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCCTACGCGGGTCATAGTTgg                                                                                                                                                                                                   >  1:39189/2‑148 (MQ=255)
                                                                                   ncAAATACAAAACCAATTTCAGCCAGTGCCTCGTCCATTTTTTCGATGAACTCCGGCACGATCTCGTCAAAACTCGCCATGTACTTTTCATCCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTc                                                                                                                                                                              >  1:96855/2‑169 (MQ=255)
                                                                                    tccaatctaaaCCAATTTCAGCCAGTGCCTCGTCCATTTTTTCGATGAACTCCGGCACGATCTCGTCAAAACTCGCAATGTACTTTTCATCCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCTGACTTTATGGCCTCGAACCCACCGAGCCGGAACTTCATGaa                                                                                            <  1:11868/242‑1 (MQ=255)
                                                                                    cAAATACAAAACCAATGTCAGCCAGTGCCGCGTCCATGTTTGCGATGAACTCCGGCACGAGCTCGTCAAAACTCGCCATGTACTTTTCATCCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATACGCGGGTCATAGTTGGCAAAGTa                                                                                                                                                                                            <  1:160010/154‑1 (MQ=255)
                                                                                          cAAAACCAATTGCATCCAGTGCCTCGTCCATTGTGTCGATGAACTCCGGCACCATCTCGTCAAAACTCGCCATGTGCTTTTCATGCCGCTCAATCGCGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCagct                                                                                                                                                                                              <  1:291562/146‑4 (MQ=255)
                                                                                            aaaCCAATTTCAGCCAGTGCCTCGTCCATTTTTTCGATGAACTCCGGCACGATCTCGTCAAAACTCGCCATGTACTTTTCATCCCGCTNNATCACg                                                                                                                                                                                                                                              >  2:11868/1‑96 (MQ=255)
                                                                                                cAATTTCAGCCAGTGCCTCGTCCATTTTATCGATGAACTCCGGCACCATCTCGTCAAAACTCGCCATGTACTTGTCATTCCGCTCAATCACGACATAAGGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCATGCATCTTTTCGCGTCAGCCACATACTGTACTGCACCTGGGCCGTGTAAGCCGATTTTATTGCCTCGAAACCACCg                                                                                                             <  1:50341/221‑1 (MQ=255)
                                                                                                  aTTTCAGCCAGTGCCTCGTCCATTTTTTCGATGAACTCCGGCACGATCTCGGCAAAACTCGCCATGTACGTTTCAGCCCGCTCAATCACGTCATAATGCAGGCCTTCACGCTTCATACGCGGGTCATAGTTGGCAAAGt                                                                                                                                                                                             <  1:324373/139‑1 (MQ=255)
                                                                                                        gCCAGTGCNTNNNCNNTTTTTTCGATGAACTCCGGCACCATCTCGTCAAAACTCGCCATGNACTTTTCATTCCGATNAANCACGNCATNATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTc                                                                                                                                                                              >  2:226201/1‑148 (MQ=255)
                                                                                                        gCCAGTGCCTCGTCCATTTTTTCGATGAACTCCGGCTCCATCTCGGCAAAACTCGCCATGTACATGTCATTCCTCTCTAACACTACATAATGCAGTCCGTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTc                                                                                                                                                                              <  1:226201/148‑1 (MQ=255)
                                                                                                                cTCGTCCATTTTTTCGATGAACTCCGGCACGATCTCGTCAAAACTCGCCATGTACTTTTCATCCCGCTCAATCACGACATAATGCAGGCCTTCACGATTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCTGACTTTATGGCCTTGAAACCACCGAGCCGGAACTTCATGAAATCCCGGGAGGTaaacgggcatttcagtt                                                               >  1:69164/1‑235 (MQ=255)
                                                                                                                             tCGATGAACTCCGGCACCATCTCGTCAAAACTCGCCATGTACTGTTCAGTCCGCTCAATCACTACATAATGCAGGCCTGCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAg                                                                                                                                                                                        <  1:163835/117‑1 (MQ=255)
                                                                                                                                  gAACTCCGGCACCATCTCGTCAAAACTCGCCATGTACTTTTCATTCCGCTCCATCACGACCTAATGCGGGCCTTCACGCTTCATGAGCGGGTCATAGTTGGCAAAGTAGCAGGCa                                                                                                                                                                                     >  1:207407/1‑115 (MQ=255)
                                                                                                                                                              nccATNTANTTTTCATTCCGCTCANTCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGNNGNNNANGTACCAgg                                                                                                                                                                                       <  2:228850/84‑1 (MQ=255)
                                                                                                                                                              gCCATGTACTTTTCATTCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAgg                                                                                                                                                                                       >  1:228850/1‑85 (MQ=255)
                                                                                                                                                                              tCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGAATCTTTTCTCGTCACCCACATGGTGTACTGCACCTTGGCCATGTAAGCCGAGTTGATTGCCTCGAATCTACCGAGCCGGATTTTCAGGAAATCCCGGGATGTATGAGTATTGCCTGTATCGTGTTCGGGAGTCGGATGCTTAGTCTTATCCGTGGAAATCGACCGCGCATTACtggttgg  <  1:218471/250‑1 (MQ=255)
                                                                                                                                                                              |                                                                                                                                                                                                                                                         
GAGACTGAAGCGCCGCAATGCAGGCTTGCCGTGTTGTGAGGTACCCGGATATTATCGTGAGGATGCGTCATCGCCATTGCTCCCCAAATACAAAACCAATTTCAGCCAGTGCCTCGTCCATTTTTTCGATGAACTCCGGCACCATCTCGTCAAAACTCGCCATGTACTTTTCATTCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGAGGTACGAGTATTGCCGGAAGCGTGGCCTGTATCCGGATGCAGAGTCTTATCCGTGGAAATCGAACGCGCATTACTGGTTGG  >  NC_000913/566031‑566454

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑