Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913753,1250TA28.6% 74.7 / 10.6 35intergenic (‑330/+60)ybgD/gltAputative fimbrial‑like adhesin protein/citrate synthase
Reads supporting (aligned to +/- strand):  ref base T (23/2);  new base A (0/10);  total (23/12)
Fisher's exact test for biased strand distribution p-value = 3.60e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

TTGTTGTATGATGAATAAAATATAGGGGGGTATAGATAGACGTCATTTTCATAGGGTTATAAATGCGACTACCATGAAGTTTTTAATTGAAAGTATTGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTTAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTT‑GTGTTT‑AGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACAGCTGACGCGGACGGGCAATCTTCATACCGTCACTGTGCATTTCGCTCCAGTGGGCGATCCAGCCAACGGTACGTGCCATTGCGAAAATGACGGTGAACATGGAAG  >  NC_000913/752933‑753339
                                                                                                                                                                                                  |                                                                                                                                                                                                                      
ttgttgTATGATGAATAAAATATAGGGGGGTATAGATAGACGTCATTTTCATAGGGTTATAAATGCGACTACCATGAAGTTTTTAATTGAAAGTATTGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTTAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTT‑GTGTTT‑AGGCATATAAAAATCAACCCGCCATATGAATGGCGGGGTTATATATTTTTAACt                                                                                                                                                                          >  2:245761/1‑239 (MQ=255)
       atgatgAATAAAATATAGGGGGGTATAGATAGACGTCATTTTCATAGGGTTATAAATGCGACTACCATGAAGTTTTTAATTGAAAGTATTGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTTAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTT‑GTGTTT‑AGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTTAAATATTTACAACTTTGCaa                                                                                                                                                                    >  1:50472/1‑238 (MQ=255)
             aaTAAAATATAGGGGGGTATAGATAGACGTCATTTTCATAGGGTTATAAATGCGACTACCATGAAGTTTTTAATTGAAAGTATTGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTTAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTT‑GTGTTT‑AGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTTAAATATTTACAACTTATCCATCAACCa                                                                                                                                                             >  1:637074/1‑239 (MQ=255)
                    tataGGGGGGTATAGATAGACGTCATTTTCATAGGGTTATAAATGCGACTACCATGAAGTTTTTAATTGAAAGTATTGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTTAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTT‑GTGTTT‑AGGCATATAAAAATCAACCCGCCATATGa                                                                                                                                                                                                   >  1:476662/1‑194 (MQ=255)
                              tataGATAGACGTCATTTTCATAGGGTTATAAATGCGACTACCATGAAGTTTTTAATTGAAAGTATTGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTTAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTT‑GTGTTT‑AGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATc                                                                                                                                              >  1:797815/1‑237 (MQ=255)
                                     agaCGTCATTTTCATAGGGTTATAAATGCGACTACCATGAAGTTTTTAATTGAAAGTATTGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTTAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTT‑GTGTTT‑AGGCATATAAAAATCAACCCGCCATATGAACGGCGGGGTTAAATATTTAAAAATTAGCAATCAACCATTTAAGCTTTATATTGCTTTTtaa                                                                                                                                     >  2:257319/1‑239 (MQ=255)
                                            aTTTTAATAGGTTTAAAAATGCGATGACAATAAAGTTTTTATTTGAAAGTTTTGGGTTGTTAATATTTTGATTTTTTTTTTTTTTTTAAAATATTTATAAGGTTCTTTTAATGAATTTTATTTTAAAAATTTTTT‑GTTTTA‑CGAAATAAAAAAATCACCCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGt                                                                                                                              <  2:797815/239‑1 (MQ=255)
                                                 aatgggtttATAAAGGCAATTACAATAAATTTTTAAATTAAAAGTTTTGGGTGGCTAATAATTTGGGTTTTTTTTTTTTTTTAAAATATTTATATAGGTTTGTAAATGGATTTTATTTTAAAAATTTTTT‑GTGTTA‑AGAAAAAAAAAAAACAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTc                                                                                                                         <  2:50472/232‑1 (MQ=255)
                                                                 cGACTACCATGAAGTTTTTAATTGAAAGTATTGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTTAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTT‑GTGTTT‑AGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTaaaa                                                                                                                                                                                     >  2:543189/1‑163 (MQ=255)
                                                                               tttttAATTAAAAGTATGGGTTTGTGTATATTTTTGTCTTTTTTTTTTTTTTTAAATTTTTAATTAGGTTTATAAATGGTTTTTTTTTTTACATTTTTTT‑GTTTTT‑AGGCAAAAAAAAAACAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACAGCTGACGCGGACGGGc                                                                                           <  2:527504/239‑1 (MQ=255)
                                                                                 tttAATTGAAAGTATTGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTTAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTT‑GTGTTT‑AGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTTAAATCGCGTTTTTCATATCCTGTATACAGCTGACGCGGACGGGc                                                                                           >  1:527504/1‑237 (MQ=255)
                                                                                         aaaGTATTGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTTAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTT‑GTGTTT‑AGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGata                                                                                                                                                >  1:559157/1‑176 (MQ=255)
                                                                                                                 gAGCTGTTCTACTCTTTTTAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTT‑GTGTTT‑AGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAAAGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACAGCTGACGCGGACGGGCAATCTTCCTACCGTCACTGTGCATTTTGCTCCAg                                                         >  1:842037/1‑239 (MQ=255)
                                                                                                                     tGTTCTTTTCTTTTAAAATATTATTATAGGTCTGTTAATGGATTTTTTTTTTAAAATTTTTT‑‑TGTTTAAGGGATAAAAAAACCACCCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACAGCTGACGCGGACGGGCAATCTTCATACCGTCACTGTGCATTTCGCTCCAGTgg                                                      <  1:245761/238‑1 (MQ=255)
                                                                                                                                 ttaaaaTATCTATATAGGTTTGTTAATGTTTTTTATTTTTACAATTTTTT‑GTTTTT‑AGGAATAAAAAAACCACCCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACAGCTGACGCGGACGGGCAATCTTCATACCGTCACTGTGCATTTCGCTCCAGTGGGCGATCCAGCCaa                                         <  1:257319/236‑1 (MQ=255)
                                                                                                                                  ttAAATTTTTATATATGTTTGTTAATGAGTTTTATTTTTTAAATTTTTTGGTTTTT‑AACCATAAAAAAACCACCCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACAGCTGACGCGGACGGGCAATCTTCATACCGTCACTGTGCATTTCGCTCCAGTGGGCGATCCAGCCaa                                         <  2:842037/239‑1 (MQ=255)
                                                                                                                                             aatggtttttttAATGG‑TTTTTTTTTTGAAATTTTTT‑GTTTTTAAGGAAAAAAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACAGCTGACGCGGACGGGCAATCTTCATACCGTCACTGTGCATTTCGCTCCAGTGGGCGATCCAGCCAACGGTACGTGCCa                             <  2:751583/229‑1 (MQ=255)
                                                                                                                                                  gTCTGTTAATGGATTTTATTTTTACAATTTTTT‑GTGTTT‑AGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCCACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACAGCTTACGCGGACGGGCAATCTTCATACCGTCACTGTGCATTTCGCTCCCGTGGGGGATCCAGCCAACGCTACGCGCCCTTGCg                        >  1:708181/1‑239 (MQ=255)
                                                                                                                                                  gTCTGTTAATGGATTTTATTTTTACAATTTTTT‑GTGTTT‑AGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCAAATCCTGTATACAGCTGACGCGGACGGGCAATCTTCATACCGTCACTGTGCATTTCGCTCCAGTGGGCGATCCAGCCCACGATa                                    >  1:569492/1‑227 (MQ=255)
                                                                                                                                                   tCTTTTAATGGATTTTTTTTTTAAATTTTTTT‑GTGTTT‑AGGAATAAAAAAACCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACAGCTGACGCGGACGGGCAATCTTCATACCGTCACTGTGCATTTCGCTCCAGTGGGCGATCCAGCCAACGGTACGTGcc                              <  1:40618/232‑1 (MQ=255)
                                                                                                                                                     tGTTAATGGATTTTATTTTTACAATTTTTT‑GTGTTT‑AGGCATATAAAAATCAACCCGCCATATGAACGGCGGGGTAAAATATTTTAAAATTAGCAAACAACCATTAAAGCCTGATAACGCTTTTAAAGTCGCGGTTTTTATATCCTGTATACAACTGAAGCGGGCGGGGCATTCTCATACCGTTACagtg                                                                      >  1:715759/1‑190 (MQ=255)
                                                                                                                                                     tGTTAATGGATCTTATTTTTACAATTTTTT‑GTGTTT‑AGGCATATAAAAATCAACCCGCCATATGAACGGCGTGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACAGCTGACGCGGACGGGCAATCTTCATa                                                                                 >  1:827640/1‑179 (MQ=255)
                                                                                                                                                       ttAATGGATTTTATTTTTACAATTTTTT‑GTGTTT‑AGGCATATAAAAATCAACCCGCCATATGAAcgg                                                                                                                                                                                               >  2:857261/1‑67 (MQ=255)
                                                                                                                                                       ttAATGGATTTTATTTTTACAATTTTTT‑GTGTTT‑AGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTCAAATCTTTACAACTTAGCAATCAACCATTAACGCTTGATATAGCTTTTAAAGTCGCGTTTTTCTTATTCTTTATTCACCTGATCCGGATGGGCAATCTTCATTCCGTTACTATTACTTTTGTCCTAGCGGGGGGTACCGCCCAATGTACGTCCCATTGCGCAAAt                   >  2:64985/1‑239 (MQ=255)
                                                                                                                                                       ttAATGGATTTTATTTTTACAATTTTTT‑GTGTTT‑AGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTTAAGTCGCGTTTTTCATATCCTGTATACAGCTGACGCGGACGGGCAATCTTCATACCGTCACTGTGCATTTCGCTCCCGTGGGGGATCCAGCCCACCGTACCTGCCCTTTCGgaaaa                   >  2:40618/1‑238 (MQ=255)
                                                                                                                                                       ttAATGGATTTTATTTTTACAATTTTTT‑GTGTTT‑AGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACAGCTGACGCGGACGGGCAATCTTCATACCGTCACTGTGCATTTCGCTCCAGTGGGCGATCCAGCCAACGGTACGTGCCATTGCGAAAAt                   >  1:751583/1‑239 (MQ=255)
                                                                                                                                                       ttAATGGATTTTATTTTTACAATTTTTT‑GTGTTT‑AGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTAAAAATTAGCAAACAACCATTAACGCTTTATATCGCTTTTAAAGTCGCGGTTTTCATATCCTGta                                                                                                               >  1:241820/1‑147 (MQ=255)
                                                                                                                                                       ttAAGGGATTTTATTTTTACAATTTTTT‑GTTTTT‑AGGCATATAAAAATCAACCCGCCATATGAAcgg                                                                                                                                                                                               <  1:857261/67‑1 (MQ=255)
                                                                                                                                                            ggATTTTATTTTTACAATTTTTT‑GTGTTT‑AGGCATATAAAAATCAACCCGCCATATGAATGGCGGGTTTAAATGTTTATTAATTCGCCATCAACCATTCACGCTTTTATTCACTTTTAAAGCCGCCTATTTCTAATCCTGTATACAGCTTTAGCGGACGGGCAATCTTCATTCCGTCACTTTGCATTTCGCCCCAGTGGGGGAACCAGCCAACGGTACGCGCCCTTGCGAAAATTAcag              >  2:698183/1‑237 (MQ=255)
                                                                                                                                                               ttttattttTACAATTTTTT‑GTGTTT‑AGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATAGTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACAGCTGACGCGGACGGGCAATCTTCATAc                                                                                >  1:813786/1‑170 (MQ=255)
                                                                                                                                                                 ttattttTACAATTTTTT‑GTGTTT‑AGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAAACAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACAGCTGACGCGGACGGGCAATCTTCATACCGTCACTGTGCATTTCGCTCCAGTGGGCGATCCAGCCAACGGTACGTGCCATTGCGAAAATGACGGCGAAc         >  1:392213/1‑239 (MQ=255)
                                                                                                                                                                        taaaaTTTTTT‑GTTTTT‑GGGAATAAAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACAGCTGACGCGGACGGGCAATCTTCATACCGTCACTGTGCATTTCGCTCCAGTGGGCGATCCAGCCAACGGTACGTGCCATTGCGAAAATGACGGTGAACATGGAAg  <  1:698183/236‑1 (MQ=255)
                                                                                                                                                                              ttttt‑tTGTTG‑AGGCAAAAAAAAAACAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACAGCTGACGCGGACGGGCAATCTTCATACCGTCACTGTGCATTTCGCTCCAGt                                                        <  2:561421/179‑1 (MQ=255)
                                                                                                                                                                                     tgtTT‑AGGAAAATAAAAATCCCCCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACAGCTGACGCGGACGGGCAATCtt                                                                                     <  2:746717/144‑1 (MQ=255)
                                                                                                                                                                                         t‑AGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACCTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGGTTTTCATATCCTGTATACAGCTGACGCGGACGGGCAATCTTCATACCGTCACTGTGCATTTCGCTCCAGTGGGCGATCCa                                              >  1:561421/1‑179 (MQ=255)
                                                                                                                                                                                                tataAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCCACCATTAACACTTGATATCGCTTTTAAAGTCGCGTTTTTCCTATCCCGTATTCAGCCAACGCGGACGGGCAAACTTCATaacctcc                                                                           >  1:746717/1‑138 (MQ=255)
                                                                                                                                                                                                  |                                                                                                                                                                                                                      
TTGTTGTATGATGAATAAAATATAGGGGGGTATAGATAGACGTCATTTTCATAGGGTTATAAATGCGACTACCATGAAGTTTTTAATTGAAAGTATTGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTTAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTT‑GTGTTT‑AGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACAGCTGACGCGGACGGGCAATCTTCATACCGTCACTGTGCATTTCGCTCCAGTGGGCGATCCAGCCAACGGTACGTGCCATTGCGAAAATGACGGTGAACATGGAAG  >  NC_000913/752933‑753339

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑