Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,649,2950TG47.5% 56.3 / 11.9 40intergenic (+254/‑314)ydfC/dicBuncharacterized protein, Qin prophage/Qin prophage; cell division inhibition protein
Reads supporting (aligned to +/- strand):  ref base T (2/19);  new base G (19/0);  total (21/19)
Fisher's exact test for biased strand distribution p-value = 1.61e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATTTCCCTGAAAAGTCAGACCATAACGCGAAAGCGCATGGCGAGGTAGCTGGTTCATAGATAGCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGCGGGGTTATTCCTTCCCCGTTGAGGACA‑CCGGGTTGTCAGGTTGACCATACGCTTAAGTGACAACCCCGCTGCAACGCCCTCTGTTATCAATTTTCTGGTGACGTTTGGCGGTATCAGTTTTACTCCGTGACTGCTCTGCCGCCCTTTT  >  NC_000913/1649153‑1649438
                                                                                                                                              |                                                                                                                                                
atTTCCCTGAAAAGTCAGACCATAACGCGAAAGCGCATGGCGAGGTAGCTGGTTCATAGATAGCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGCGGGGTTAttcct                                                                                                                                           <  2:149406/150‑1 (MQ=255)
 tttCCCTGAAAAGTCAGACCATAACGCGAAAGCGCATGGCGAGGTAGCTGGTTCATAGATAGCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGCGGGGGTAtttctt                                                                                                                                          >  1:450586/1‑150 (MQ=255)
       tGAAAAGTCAGACCATAACGCGAAAGCGCATGGCGAGGTAGCTGGTTCATAGATAGCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGCGGGGGGTTTTCTTcccc                                                                                                                                      >  2:747421/1‑148 (MQ=255)
        gAAAAGTCAGACCATAACGCGAAAGCGCATGGCGAGGTAGCTGGTTCATAGATAGCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGCGGGGTTATTCCTTCCCCGtt                                                                                                                                   <  2:189191/150‑1 (MQ=255)
         aaaaGTCAGACCATAACGCGAAAGCGCATGGCGAGGTAGCTGGTTCATAGATAGCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGCGGGGGTATTTCTTcccc                                                                                                                                      >  1:143129/1‑146 (MQ=255)
                aGACCATAACGCGAAAGCGCATGGCGAGGTAGCTGGTTCATAGATAGCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGCGGGGGTATTTCTTcccc                                                                                                                                      >  1:534565/1‑139 (MQ=255)
                 gACCATAACGCGAAAGCGCATGGCGAGGTAGCTGGTTCATAGATAGCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGCGGGGGGTTTTCTTTCCCCTTGAgggaacc                                                                                                                          >  2:218678/1‑145 (MQ=255)
                  aCCATAACGCGAAAGCGCATGGCGAGGTAGCTGGTTCATAGATAGCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGCGGGGTTATTCCTTCCCCGTTGAGGACA‑CCgg                                                                                                                       <  1:803008/151‑1 (MQ=255)
                   ccATAACGCGAAAGCGCATGGCGAGGTAGCTGGTTCATAGATAGCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGCGGGGTTATTCCTTCCCCGTTGAGGACA‑CCggg                                                                                                                      <  1:820914/151‑1 (MQ=255)
                   ccATAACGCGAAAGCGCATGGCGAGGTAGCTGGTTCATAGATAGCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGCGGGGGTTTTTCTTCCCCCTTgggggaacccgg                                                                                                                       >  1:339169/1‑143 (MQ=255)
                      tAACGCGAAAGCGCATGGCGAGGTAGCTGGTTCATAGATAGCCTGTCGTTAAATTTTCGTCGACCGTGCGCTCCCGGTTGTGGCAACCCGCGCAATGGCGCGGCGGTAAGCATGGCGGCGGTTTTTCTTTCCCGTTGAGGACA‑CCcgggt                                                                                                                    >  1:684401/1‑148 (MQ=255)
                            gAAAGCGCATGGCGAGGTAGCTGGTTCATAGATAGCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGCGGGGGTATTTCTTCCCCCCTGAGGGCA‑CCCGGGTGTCAgg                                                                                                              >  2:391965/1‑150 (MQ=255)
                                  gcATGGCGAGGTAGCTGGTTCATAGATAGCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGCGGGGGTATTTCCTCCCCCTTTGGGACA‑CCCGGGTGGCAggcttaacc                                                                                                       >  1:842927/1‑144 (MQ=255)
                                      ggCGAGGTAGCTGGTTCATAGATAGCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGCGGGGTTATTCCTTCCCCGTTGAGGACA‑CCGGGTTGTCAGGTTGACCATACg                                                                                                   <  1:333116/151‑1 (MQ=255)
                                          aGGTAGCTGGTTCATAGATAGCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGCGGGGGTATTTCTTCTCCGCTGGGGACA‑ACCGGGTGGCAGGTTGACCATACGcct                                                                                                >  1:537173/1‑148 (MQ=255)
                                                cTGGTTCATAGATAGCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGCGGGGGTATTTCTTCCCCCCTGTGGGCA‑CCCGGGTGTTAGGGTGAGCATAcccctta                                                                                              >  2:796863/1‑140 (MQ=255)
                                                     tCATAGATAGCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGCGGGGGTATTTCTTCCCCCTTTGGGACA‑CCGGGGTGTCAGGGTGACCATACGCCTAAATGACAAacc                                                                                    >  1:714356/1‑151 (MQ=255)
                                                         agatagCCTGTTGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGCGGGGTTATTCCTTCCCCGTTGAGGACA‑CCGGGTTGTCAGGTTGACCATACGCTTAAGTGACAACCCCGCt                                                                                <  1:532065/151‑1 (MQ=255)
                                                                cTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGCGGGGGTTTTTTTTTCCCGGTGTGGACA‑CCGGGGTGTCTGGGTGACCCTAAGCCTAAGTGACAACCCCCCTGCAAccc                                                                         >  1:555564/1‑149 (MQ=255)
                                                                       tAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGCGGGGGTTTTTCTTTCCCCCTGGGGACACCCGGGTTTTC‑GGGTGACCATTCGCTTAAATGAGCACACCCCTGCTAAGccccc                                                                     >  2:39459/1‑146 (MQ=255)
                                                                        aaaTTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGCGGGGTTATTCCTTCCCCGTTGAGGACA‑CCGGGTTGTCAGGTTGACCATACGCTTAAGTGACAACCCCGCTGCAACGCCCTCTGt                                                                  <  2:745466/150‑1 (MQ=255)
                                                                            tttCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGCGGGGTTATTCCTTCCCCGTTGAGGACA‑CCGGGTTGTCAGGTTGACCATACGCTTAAGTGACAACCCCGCTGCAACGCCCTCTGTTATc                                                              <  1:489739/150‑1 (MQ=255)
                                                                              tcgtcgACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGCGGGGTTATTCCTTCCCCGTTGAGGACA‑CCGGGTTGTCAGGTTGACCATACGCTTAAGTGACAACCCCGCTGCAACGCCCTCTGTTATCaa                                                            <  1:385284/150‑1 (MQ=255)
                                                                               cgtcgACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGCGGGGTTATTCCTTCCCCGTTGAGGACA‑CCGGGTTGTCAGGTTGACCATACGCTTAAGTGACAACCCCGCTGCAACGCCCTCTGTTATCAAt                                                           <  1:855486/150‑1 (MQ=255)
                                                                                  cgACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGCGGGGTTATTCCTTCCCCGTTGAGGACA‑CCGGGTTGTCAGGTTGACCATACGCTTAAGTGACAACCCCGCTGCAACGCCCTCTGTTATCAAtttt                                                        <  2:607541/150‑1 (MQ=255)
                                                                                    aCCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGGGGGGTTATTCCTTCCCCATTGAGGACA‑CCGGGTTGTCAGGTTGACCATACGCTTAAGTGACAGCCCCGGTGCAACGCCCTCTGTTATCAATTTTCt                                                      <  2:802583/150‑1 (MQ=255)
                                                                                         gcgcTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGCGGGGTTATTCCTTCCCCGTTGAGGACA‑CCGGGTTGTCAGGTTGACCATACGCTTAAGTGACAACCCCGCTGCAACGCCCTCTGTTATCAATTTTCTGGTGa                                                 <  2:450088/150‑1 (MQ=255)
                                                                                           gcTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGCGGGGGTTTTTCTTCCCCCCTGAGGGCA‑CCCGGGTGTCAAGTTGACCATACGCTTTAGTGGCAACCCCCCCGCCACGCCCCCTGTTTTCAAttttttt                                                     >  2:145041/1‑141 (MQ=255)
                                                                                                cGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGCGGGGTTATTCCTTCCCCGTTGAGGACA‑CCGGGTTGTCAGGTTGACCATACGCTTAAGTGACAACCCCGCTGCAACGCCCTCTGTTATCAATTTTCTGGTGACGTTTGGc                                         <  2:114430/151‑1 (MQ=255)
                                                                                                  gTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGCGGGGGTATTTCTTCCCCGGTGAGGGCA‑CCCGGGTGTTAGGGTGACCATACGCTTAAGTGACAACCCCCCTGCAACGCCCCCTGTTTTCAATTTTTTTGGGGCGTTTGgggg                                       >  1:59790/1‑151 (MQ=255)
                                                                                                    tgtgGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGCGGGGTTATTCCTTCCCCGTTGAGGACA‑CCGGGTTGTCAGGTTGACCATACGCTTAAGTGACAACCCCGCTGCAACGCCCTCTGTTATCAATTTTCTGGTGACGTTTGGCGGt                                      <  1:300461/150‑1 (MQ=255)
                                                                                                       ggCAACCCGCGAAATGGCGCGGCGGTAAGTATGGCGGGGTTATTCCTTCCCCGTTGAGGACA‑CCGGGTTGTCAGGTTGACCATACGCTTAAGTGACAACCCCGCTGCAACGCCCTCTGTTATCAATTTTCTGGTGACGTTTGGCGGTATCa                                  <  1:753102/151‑1 (MQ=255)
                                                                                                             ccGCGAAATGGCGCGGCGGTAAGTATGGCGGGGTTATTCCTTCCCCGTTGAGGACA‑CCGGGTTGTCAGGTTGACCATACGCTTAAGTGACAACCCCGCTGCAACGCCCTCTGTTATCAATTTTCTGGTGACGTTTGGCGGTATCAGTTTTa                            <  1:29009/151‑1 (MQ=255)
                                                                                                                    aTGGCGCGGCGGTAAGTATGGCGGGGTTATTCCTTCCCCGTTGAGGACA‑CCGGGTTGTCAGGTTGACCATACGCTTAAGTGACAACCCCGCTGCAACGCCCTCTGTTATCAATTTTCTGGTGACGTTTGGCGGTATCAGTTTTACTCCGTg                     <  1:274148/151‑1 (MQ=255)
                                                                                                                    aTGGCGCGGCGGTAAGTATGGCGGGGTTATTCCTTCCCCGTTGAGGACA‑CCGGGTTGTCAGGTTGACCATACGCTTAAGTGACAACCCCGCTGCAACGCCCTCTGTTATCAATTTTCTGGTGACGTTTGGCGGTATCAGTTTTACTCCGTg                     <  2:339133/151‑1 (MQ=255)
                                                                                                                    aTGGCGCGGCGGTAAGTATGGCGGGGGTATTTCTTTCCCCGTGTGGACA‑CCCGGGTGTCAGGGTGACCCTACGCCTAAGTGACAACCCCCCTGCAAAGCCCCCTGTTATCAATTTTTTGGTGGCGTTTGGCGGGATCAGTTTTTCTCCCTg                     >  1:285172/1‑151 (MQ=255)
                                                                                                                    aTGGCGCGGCGGTAAGTATGGCGGGGGTATTTCTTCCCCCCTGAGGACA‑CCGGGGTGTCAGGGTGACCCTACGCTTAAGTGACAAACCCCCTGCAACGCCCTCTGTTTTCAATTTTTTGGTGACGTTTTGCGGGATCAGTTTTTCTcc                        >  1:560547/1‑148 (MQ=255)
                                                                                                                               gTAAGTATGGCGGGGGTATTCCTTCCCCGTTGAGGACA‑ACGGGGTGGCAGGTTGACCCTACGCTTAAGTGGCAACCCCCCTGCCACGGCCCCTGTTTTTAATTTTTTTGTGACGTTTTGCGGTGTTAGTTTTACTCCCTg                     >  2:55820/1‑140 (MQ=255)
                                                                                                                                   gTATGGCGGGGTTATTCCTTCCCCGTTGAGGACA‑CCGGGTTGTCAGGTTGACCATACGCTTAAGTGACAACCCCGCTGCAACGCCCTCTGTTATCAATTTTCTGGTGACGTTTGGCGGTATCAGTTTTACTCCGTGACTGCTCTGCCGccc      >  1:398206/1‑151 (MQ=255)
                                                                                                                                       ggCGGGGTTATTCCTTCCCCGTTGAGGACA‑CCGGGTTGTCAGGTTGACCATACGCTTAAGTGACAACCCCGCTGCAACGCCCTCTGTTATCAATTTTCTGGTGACGTTTGGCGGTATCAGTTTTACTCCGTGACTGCTCTGCCGCCCtttt  >  1:789828/1‑151 (MQ=255)
                                                                                                                                              |                                                                                                                                                
ATTTCCCTGAAAAGTCAGACCATAACGCGAAAGCGCATGGCGAGGTAGCTGGTTCATAGATAGCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGCGGGGTTATTCCTTCCCCGTTGAGGACA‑CCGGGTTGTCAGGTTGACCATACGCTTAAGTGACAACCCCGCTGCAACGCCCTCTGTTATCAATTTTCTGGTGACGTTTGGCGGTATCAGTTTTACTCCGTGACTGCTCTGCCGCCCTTTT  >  NC_000913/1649153‑1649438

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑