Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,678,3850TA39.3% 43.0 / 11.0 28intergenic (‑35/+35)yhjG/yhjHputative inner membrane‑anchored periplasmic AsmA family protein/cyclic‑di‑GMP phosphodiesterase, FlhDC‑regulated
Reads supporting (aligned to +/- strand):  ref base T (13/4);  new base A (0/11);  total (13/15)
Fisher's exact test for biased strand distribution p-value = 6.72e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGATAGTCGGTTTGAGTCGATTCCAGTCAAAAGTTGCAATCAAAATGATCGCCACGACAATCAACAACAAGAAAGCCCCTGAAATCGCAGCGGTTATTTTGCCTGCCTTGCT‑CATCGTTCGCTTCCTCATATTCTTCCTGTGCCAGTCCTAAAGATAGTCCAGCCAGGCGGAAAATGAGGCAGCTTATAGCGCCAGAACCGCCGTATTCAGCGTTTCTATCGGTGCCGGGCGTGAAAGAAACCAGCCTTGTGCGGCGAATGCGGGCGAGTTCTGAACATCAC  >  NC_000913/3678236‑3678517
                                                                                                                                                      |                                                                                                                                    
tGATAGTCGGTTGGAGTCGATTCCAGGCAAAAGTTGCAATCAAAATGATCGCCACGACAATCAACAACAAGAAAGCCCCTGAAATCGCAGCGGTGATTTTGCCTGCCTTGCT‑CATCGTTCGCTTCCTCATATTCTTCCTGTGCCAGTCCt                                                                                                                                      <  1:134826/150‑1 (MQ=255)
                tCGATTCCAGTCAAAAGTTGCAATCAAAATGATCGCCACGACAATCAACAACAAGAAAGCCCCTGAAATCGCAGCGGTTATTTTGCCTGCCTTGCT‑CATCGTTCGCTTCCTCATATTCTTCCTGTGCCAGTCCTAAAGATAGTccagcc                                                                                                                       >  2:231241/1‑149 (MQ=255)
                 cGATTCCAGTCAAAAGTTGCAATCAAAATGAGCGCCACGACAATCAACAACAAGAAAGCCCCTGAAATCGCAGCGGTTATTTTGCCTGCCTTGCT‑CATCGTTCGCTTCCTCATATTCTTCCTGTGCCAGTCCTAAAGATAGTccagccag                                                                                                                     <  1:325468/150‑1 (MQ=255)
                    ttCCAGTCAAAAGTTGCAATCAAAATGATCGCCACGACAATCAACAACAAGAAAGCCCCTGAAATCGCAGCGGTTATTTTGCCTGCCTTGCT‑CATCGTTCGCTTCCTCATATTCTTCCTGTGCCAGTCCTAAAGATAGTCCAGCCAGGCgg                                                                                                                 >  2:575191/1‑151 (MQ=255)
                                        cAAAATGATCGCCACGACAATCAACAACAAGAAAGCCCCTGAAATCGCAGCGGTTATTTTGCCTGCCTTGCT‑CATCGTTCGCTTCCTCATATTCTTCCTGTGCCAGTCCTAAAGATAGTCCAGCCAGGCGGAAAATGAGGCAGCTTATAg                                                                                              <  1:281772/150‑1 (MQ=255)
                                        cAAAATGATCGCCACGACAATCAACAACAAGAAAGCCCCTGAAATCGCAGCGGTTATTTTGCCTGCCTTGCT‑CATCGTTCGCTTCCTCATATTCTTCCTGTGCCAGTCCTAAAGATAGTCCAGCCAGGCGGAAAATGAGGCAGCTTATAg                                                                                              <  2:194157/150‑1 (MQ=255)
                                            aTGATCGCCACGACAATCAACAACAAGAAAGCCCCTGAAATCGCAGCGGTTATTTTGCCTGCCTTGCT‑CATCGTTCGCTTCCTCATATTCTTCCTGTGCCAGTCCTAAAGATAGTCCAGCCAGGCGGAAAATGAGGCCGCTTATAGCGcc                                                                                          >  1:259964/1‑150 (MQ=255)
                                              gATCGCCACGACAATCAACAACAAGAAAGCCCCTGAAATCGCAGCGGTTATTTTGCCTGCCTTGCT‑CATCGTTCGCTTCCTCATATTCTTCCTGTGCCAGTCCTAAAGATAGTCCAGCCAGGCGGAAAATGAGGCAGCTTATAGCGcc                                                                                          >  2:402178/1‑148 (MQ=255)
                                                 cGCCACGACAATCAACAACAAGAAAGCCCCTGAAATCGCAGCGGTTATTTTGCCTGCCTTGCT‑CATCGTTCGCTTCCTCATATTCTTCCTGTGCCAGTCCTAAAGATAGTCCAGCCAGGCGGAAAATGAGGCAGCTTATAGCGCCAGAAcc                                                                                    >  2:87367/1‑151 (MQ=255)
                                                      cGACAATCAACAACAAGAAAGCCCCTGAAATCGCAGCGGTTATTTTGCCTGCCTTGCT‑CATCGTTCGCTTCCTCATATTCTTCCTGTGCCAGTCCTAAAGATAGTCCAGCCAGGCGGAAAATGAGGCAGCTTATAGCGCCAGAACCGCCGt                                                                               >  1:388357/1‑151 (MQ=255)
                                                                     aGAAAGCCCCTGAAATCGCAGCGGTTATTTTGCCTGCCTTGCT‑CATCGTTCGCTTCCTCATATTCTTCCTGTGCCAGTCCTAAAGATAGTCCAGCCAGGCGGAAAATGAGGCAGCTTATAGCGCCAGAACCGCCGTATTCAGCGTTTCTAt                                                                >  2:41961/1‑151 (MQ=255)
                                                                       agcgCCCTTGAAACCGCAGTTTTTTTTTTGCTTCCCTCGCT‑TACGTTTCCTTTCCTCATTTTTTCCCTGGCCCATCCCAAAAGATGGCCCGCCGAGGGGAAAAGTGGGCCAGTTTATCGCCCCAGAACCGCCGTATTCAGCGTTTCTATc                                                               <  1:94789/147‑1 (MQ=255)
                                                                       aaaGCCCCTAAAACCGCGGCGGTTTTTTTCCCT‑CCTTTCTGCACCGTTCGCTTCCTCTTTTTCTTCCTGGCCCATTCCAAAAAATAGCCCAGCCAGGCGAAAAAGGGGGCGCCTTAAAGCCCAAGAACCGCCGTATTCAGCGTTTCTATCg                                                              <  1:477814/151‑1 (MQ=255)
                                                                                 aaaTCGCAGGTTTTTTTTTGCCTCCCTTGCC‑CACCGTTCCCTTCCTTATTTTCTTCCTGGGCCCGCCCTAAAAAAATTCCAGCCAGGCGAAAAATGAGGCAGCTTATGGCGCCAGAACCGCCGTATTCAGCGTTTCTATCGGTGCCgg                                                       <  2:507860/148‑1 (MQ=255)
                                                                                 aaaTCGCAGCGTTTATTTTCCCTGCTTTGCT‑CATCGTCCCCTTCCTCATTTTCTCCCTGTCCCAGCCCAAAAAATAGCCCAGCCGGGCGAAAAATGAGGCAGCTTATAGCGCCAGAACCGCCGTATTCAGCGTTTCTATCGGTGCCGGGCg                                                    <  1:110992/151‑1 (MQ=255)
                                                                                      gCAGCGGTTATTTTGCCTGCCTTGCT‑CATCGTTCGCTTCCTCATATTCTTCCTGTGCCAGTCCTAAAGATAGTCCAGCCAGGCGGAAAATGAGGCAGCTTATAGCGCCAGAACCGCCGTATTCAGCGTTTCTATCGGTGCCGGGCGTgaa                                                >  1:52660/1‑150 (MQ=255)
                                                                                         gCGTTTTTTTTGCCTGCTTTGCT‑CTTCTTTCGCTTCCTAATTTTCTCCCTGTCCCAGTCTAAAAAATAGCCCAGCAGGGCGAAAAATGGGGCAGCTTATAGCGCAAGAACCGCCGTATTCAGCGTTTCTATCGGTGCCGGGCGTgaaagaa                                            <  1:41532/151‑1 (MQ=255)
                                                                                                tttgccctgcctTGCA‑CTGCGTCCGCTCCCTCATTTTCTCCCGGGCCCAGCCCAAAAGAGGGCCCGGCCGGGGGGAAAGGGGGGCGGCTGAGAGCGCAAAAACCGCCGTATTCAGCGTTTCTATCGGTGCCGGGCGTGAAAGAAACCAg                                       <  1:171422/144‑1 (MQ=255)
                                                                                                          ctTGCT‑CATCGTTCGCTTCCTCATATTCTTCCTGTGCCAGTCCTAAAGATAGTCCAGCCAGGCGGAAAATGAGGCAGCTTATAGCGCCAGAACCGCCGTATTCAGCGTTTCTATCGGTGCCGGGCGTGAAAGAAACCAGCCTTGTgcggcg                           >  1:180560/1‑151 (MQ=255)
                                                                                                            tGCT‑CATCTTTCGCTCCCTAATATTCTTCCTGGGCCAGCCCAAAAGATAGCCCACCCGGGCGAAAAAGGGGGCGGCTTATGGCCCCAGAACCGCCGTATTCAGCGTTTCTATCGGTGCCGGGCGTGAAAGAAACCAGCCTTGTgcggcg                           <  2:170772/149‑1 (MQ=255)
                                                                                                              ct‑cctcTTTCGCTTCCTCATATTCTTCCTGTGCCAGTCCAAAAGATAGCCCAGCCAGGCGAAAAAGGAGGCAGTTTATAGCGCCAGAACCGCCGTATTCAGCGTTTCTATCGGTGCCGGGCGTGAAAGAAACCAGCCTTGTGCGGCGaa                         <  2:195472/149‑1 (MQ=255)
                                                                                                                  aTCGTTCGCTTCCTCATATTCTTCCTGTGCCAGTCCTAAAGATAGTCCAGCCAGGCGGAAAATGAGGCAGCTTATAGCGCCAGAACCGCCGTATTCAGCGTTTCTATCGGTGCCGGGCGTGAAAGAAACCAGCCTTGTGCGGCGAATGCgg                    >  2:276868/1‑151 (MQ=255)
                                                                                                                   tCGTCCGCTTCCTCATTTTCTCCCTGTCCCAGTCAAAAAGAAAGTCCAGCCAGGCGAAAAAGGAGGCAGTTTATGGCGCCAGAACCGCCGTATTCAGCGTTTCTATCGGTGCCGGGCGTGAAAGAAACCAGCCTTGTGCGGCGAATGc                      <  2:226569/148‑1 (MQ=255)
                                                                                                                    cGTTCGCTTCCTCATATTCTTCCTGTGCCAGTCCTAAAGATAGTCCAGCCAGGCGGAAAATGAGGCAGCTTATAGCGCCAGAACCGCCGTATTCAGCGTTTCTATCGGTGCCGGGCGTGAAAGAAACCAGCCTTGTGCGGCGAATGCGGGc                  >  2:118895/1‑151 (MQ=255)
                                                                                                                      ttCGCTTCCTCATATTCTTCCTGTGCCAGTCCTAAAGATAGTCCAGCCAGGCGGAAAATGAGGCAGCTTATAGCGCCAGAACCGCCGTATTCAGCGTTTCTATCGGTGCCGGGCGTGAAAGAAACCAGCCTTGTGCGGCGAATGCGGGCg                 >  2:473285/1‑150 (MQ=255)
                                                                                                                        cGCTTCCTTATTTTCTCCCTGCGCCATTCCAAAAGATACCCCAGCCGGGCGAAAAATGGGGCATCTTATGGCGCCAAACCCGCCGTATTCAGCGTTTCTATCGGTGCCGGGCGTGAAAGAAACCAGCCTTGTGCGGCGAATGCGGGCg                 <  2:810/148‑1 (MQ=255)
                                                                                                                         gCTTCCTCATATTCTTCCTGTGCCAGTCCTAAAGATAGTCCAGCCAGGCGGAAAATGAGGCAGCTTATAGCGCCAGAACCGCCGTATTCAGCGTTTCTATCGGTGCCGGGCGTGAAAGAAACCAGCCTTGTGCGGCGAATGCGGGCGAGtt             >  1:301297/1‑151 (MQ=255)
                                                                                                                           tcccTCATATTCTCCCTGGGCCATTCCAAAAGATAGCCCGGCCAGGGGGAAAATGAGGCAGTTTATAGCGCCAGAACCGCCGTATTCAGCGTTTCTATCGGTGCCGGGCGTGAAAGAAACCAGCCTTGTGCGGCGAATGCGGGCGAGtt             <  2:85869/147‑1 (MQ=255)
                                                                                                                                      ctcccTGTCCCAGTCAAAAAGATCGCCCCGCCGGGCGAAAAAGGAGGCAGTTTAGAGCCACAGAACCGCCGTATTCAGCGTTTCTATCGGTGCCGGGCGTGAAAGAAACCAGCCTTGTGCGGCGAATGCGGGCGAGTTCTGAACATCAc  <  1:213808/146‑1 (MQ=255)
                                                                                                                                                      |                                                                                                                                    
TGATAGTCGGTTTGAGTCGATTCCAGTCAAAAGTTGCAATCAAAATGATCGCCACGACAATCAACAACAAGAAAGCCCCTGAAATCGCAGCGGTTATTTTGCCTGCCTTGCT‑CATCGTTCGCTTCCTCATATTCTTCCTGTGCCAGTCCTAAAGATAGTCCAGCCAGGCGGAAAATGAGGCAGCTTATAGCGCCAGAACCGCCGTATTCAGCGTTTCTATCGGTGCCGGGCGTGAAAGAAACCAGCCTTGTGCGGCGAATGCGGGCGAGTTCTGAACATCAC  >  NC_000913/3678236‑3678517

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑