Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	566,326	0	T	C	30.9%	78.9 / 57.8	68	pseudogene (51/279 nt)	exoD	pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related
Reads supporting (aligned to +/- strand):  ref base T (26/21);  new base C (11/10);  total (37/31)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.06e-01
Rejected as consensus: Frequency below/above cutoff threshold.

TGTACTTTTCATTCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGAGGTACGAGTATTGCCGGAAGCGTGGCCTGTATCCGGATGCAGAGTCTTATCCGTGGAAATCGAACGCGCATTACTGGTTGGTTAC  >  NC_000913/566193‑566458                                                                                                                                      |                                                                                                                                     tGTACTTTTCATTCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTAt                                                                                                                                 <  1:95516/139‑1 (MQ=255)     cTTTTCATCCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCTGACTTTATGGcc                                                                                                                             <  1:91810/139‑1 (MQ=255)             tCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAacc                                                                                                                     >  1:595322/1‑139 (MQ=255)             cccGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCTGACTTTATGGCCTCGAAacc                                                                                                                     >  2:1023840/2‑139 (MQ=255)               cGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAaccac                                                                                                                   >  2:656094/1‑139 (MQ=255)               cGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCTGACTTTATGGCCTCGAAaccac                                                                                                                   <  2:825731/139‑1 (MQ=255)                gCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCATCGAAaccacc                                                                                                                  >  2:998325/1‑139 (MQ=255)                       cACGACATAATGCAGGCCTTCACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCTGACTTTATGGCCTCGAAACCACCGAGCCgg                                                                                                           <  2:197946/139‑1 (MQ=255)                           aCATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAAtt                                                                                                       >  2:725565/1‑139 (MQ=255)                              tAATGCAGGCCTTCACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCTGACTTTAtg                                                                                                                                >  1:869966/1‑110 (MQ=255)                              tAATGCAGGCCTTCACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCTGACTTTAtg                                                                                                                                <  2:869966/111‑2 (MQ=255)                                aTGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATg                                                                                                  >  2:129736/1‑139 (MQ=255)                                  gCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGaa                                                                                                <  2:558971/139‑1 (MQ=255)                                      gCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAaccac                                                                                                                   >  1:250341/1‑116 (MQ=255)                                      gCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAaccac                                                                                                                   <  2:250341/116‑1 (MQ=255)                                      gCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATcc                                                                                            >  2:413117/1‑139 (MQ=255)                                      gCCTTCACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCTGACTTTATGGCCTCGAAACCACCGAGCCGGa                                                                                                          >  2:747915/1‑125 (MQ=255)                                      gCCTTCACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCTGACTTTATGGCCTCGAAACCACCGAGCCGGa                                                                                                          <  1:747915/125‑1 (MQ=255)                                      gCCTTCACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCTGACTTTATGGCCTCGAAACCACCGAGCCGGAACTTCATGAAATcc                                                                                            <  1:514906/139‑1 (MQ=255)                                          tCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCggg                                                                                        >  2:62543/1‑139 (MQ=255)                                           cACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCTGACTTTATGGCCTCGAAACCACCGAGCCGGAACTTCATGAAATCCCGGGa                                                                                       >  2:268914/1‑139 (MQ=255)                                                ttCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCTGACTTTATGGCCTCGAAACCACCGAGCCGGAACTTCATGAAATCCCGGGAGGTaa                                                                                  >  2:731643/1‑138 (MQ=255)                                                          ggTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCTGACTTTATGGCCTCGAAACCACCGAGCCGGAACTTCATGAAATCCCGGGAGGTaaacgggcattt                                                                        >  1:1045450/1‑128 (MQ=255)                                                          ggTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCTGACTTTATGGCCTCGAAACCACCGAGCCGGAACTTCATGAAATCCCGGGAGGTaaacgggcattt                                                                        >  1:200098/1‑128 (MQ=255)                                                                 gTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGAGGTACGAGTATTGCCGGAAGCg                                                                 <  1:413117/139‑1 (MQ=255)                                                                  ttGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGAGGTACGAGTATTGCCGGAAGCGt                                                                <  2:984062/139‑1 (MQ=255)                                                                     gCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCTGACTTTATGGCCTCGAAaccac                                                                                                                   >  2:837031/1‑85 (MQ=255)                                                                     gCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCTGACTTTATGGCCTCGAAaccac                                                                                                                   <  1:837031/85‑1 (MQ=255)                                                                     gCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCTGACTTTATGGCCTCGAAACCACCGAGCCGGAACTTCATGAAATccc                                                                                           <  1:975871/109‑1 (MQ=255)                                                                     gCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCTGACTTTATGGCCTCGAAACCACCGAGCCGGAACTTCATGAAATccc                                                                                           >  1:147184/1‑109 (MQ=255)                                                                     gCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCTGACTTTATGGCCTCGAAACCACCGAGCCGGAACTTCATGAAATccc                                                                                           >  2:975871/1‑109 (MQ=255)                                                                     gCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCTGACTTTATGGCCTCGAAACCACCGAGCCGGAACTTCATGAAATccc                                                                                           <  2:147184/109‑1 (MQ=255)                                                                     gCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTAt                                                                                                                                 >  1:997960/1‑71 (MQ=255)                                                                     gCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTAt                                                                                                                                 <  2:997960/71‑1 (MQ=255)                                                                     gCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGAGGTACGAGTATTGCCGGAAGCGTGGc                                                             >  1:654536/1‑139 (MQ=255)                                                                     gCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGAGGTACGAGTATTGCCGGAAGCGTGGc                                                             >  2:583068/1‑139 (MQ=255)                                                                     gCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGAGGTACGAGTATTGCCGGAAGCGTGGc                                                             <  1:198747/139‑1 (MQ=255)                                                                     gCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGAGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGAGGTACGAGTATTGCCGGAAGCGTGGc                                                             <  1:998325/139‑1 (MQ=255)                                                                          gTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGAGGTACGAGTATTGCCGGAAGCGTGGCCTGTa                                                        >  2:381424/1‑139 (MQ=255)                                                                           tACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGAGGTACGAGTATTGCCGGAAGCGTGGCCTGTAt                                                       >  1:389567/1‑139 (MQ=255)                                                                              cAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGAGGTACGAGTATTGCCGGAAGCGTGGCCTGTATCCg                                                    <  2:595322/139‑1 (MQ=255)                                                                                ggCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGAGGTACGAGTATTGCCGGAAGCGTGGCCTGTATCCGGa                                                  >  2:235285/1‑139 (MQ=255)                                                                                   aTCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGAGGTACGAGTATTGCCGGAAGCGTGGCCTGTATCCGGATGc                                               <  2:389567/139‑1 (MQ=255)                                                                                            cgTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGAGGTACGAGTATTGCCGGAAGCGTGGCCTGTATCCGGATGCAGAGTCTTa                                      <  1:235285/139‑1 (MQ=255)                                                                                                          tGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGAGGTACGAGTATTGCCGGAAGCGTGGCCTGTATCCGGATGCAGAGTCTTATCCGTGGAAATCGa                        >  1:118712/1‑139 (MQ=255)                                                                                                            tACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGAGGTACGAGTATTGCCGGAAGCGTGGCCTGTATCCGGATGCAGAGTCTTATCCg                                  <  1:898863/127‑1 (MQ=255)                                                                                                            tACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGAGGTACGAGTATTGCCGGAAGCGTGGCCTGTATCCGGATGCAGAGTCTTATCCg                                  >  2:898863/1‑127 (MQ=255)                                                                                                            tACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGAGGTACGAGTATTGCCGGAAGCGTGGCCTGTATCCGGATGCAGAGTCTTATCCGTGGAAATCGAAc                      >  2:840339/1‑139 (MQ=255)                                                                                                            tACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGAGGTACGAGTATCGCCGGAAGc                                                                  <  1:1065108/95‑1 (MQ=255)                                                                                                            tACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGAGGTACGAGTATCGCCGGAAGc                                                                  >  2:1065108/1‑95 (MQ=255)                                                                                                             aCTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGAGGTACGAGTATTGCCGGAAGCGTGGCCTGTATCCGGATGCAGAGTCTTATCCGTGGAAATCGAAcg                     <  1:840339/139‑1 (MQ=255)                                                                                                               tGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGAGGTACGAGTATTGCCGGAAGCGTGGCCTGTATCCGGATGCAGAGTCTTATCCGTGGAAATCGAAcgcg                   <  1:386006/139‑1 (MQ=255)                                                                                                                gCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGAGGTACGAGTATTGCCGGAAGCGTGGCCTGTATCCGGATGCAGAGTCTTATCCGTGGAAATCGAACgcgc                  >  2:856257/1‑139 (MQ=255)                                                                                                                   ccTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGAGGTACGAGTATTGCCGGAAGCGTGGCCTGTATCCGGATGCAGAGTCTTATCCGTGGAAATCGAACGCGCAtt               >  1:932810/1‑139 (MQ=255)                                                                                                                     tGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGAGGTACGAGTATTGCCGGAAGCGTGGCCTGTATCCGGATGCAGAGTCTTATCCGTGGAAATCGAACGCGCATTAc             >  2:330615/1‑139 (MQ=255)                                                                                                                      gggCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCggg                                                                                        <  2:431144/63‑1 (MQ=255)                                                                                                                      gggCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCggg                                                                                        >  1:431144/1‑63 (MQ=255)                                                                                                                      gggCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGAGGTATGAGTATTGCCGGAAGCGTGGCCTGCATCCCGATGCAGAGGCTGATCCGTGGGAATCGAACGCACATTACt            >  2:1021362/1‑139 (MQ=255)                                                                                                                         ccATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGAGGTACGAGTATTGCCGGAAGCGTGGCCTGTATCCGGATGCAGAGTCTTATCCGTGGAAATCGAACGCGCATTACtggt         >  2:47321/1‑139 (MQ=255)                                                                                                                         ccATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGAGGTACGAGTATTGCCGGAAGCGTGGCCTGTATCCGGATGCAGAGTCTTATCCGTGGAAATCGAACGCGCATTACtggt         <  1:381424/139‑1 (MQ=255)                                                                                                                           aTGTAAGCCGATTTTATTGCCTCGAAATCACCCAGCCGGAATTTCATGAAATCCCGGGAGGTACGAGTATTGCCGGAAGCg                                                                 >  2:658083/1‑81 (MQ=255)                                                                                                                           aTGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGAGGTACGAGTATTGCCGGAAGCg                                                                 <  1:658083/81‑1 (MQ=255)                                                                                                                            tGTAAGCTGACTTTATGGCCTCGAAACCACCGAGCCGGAACTTCATGAAATCCCGGGAGGTaa                                                                                  <  1:548758/63‑2 (MQ=255)                                                                                                                            tGTAAGCTGACTTTATGGCCTCGAAACCACCGAGCCGGAACTTCATGAAATCCCGGGAGGTaa                                                                                  >  2:548758/1‑62 (MQ=255)                                                                                                                            tGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGAGGTACGAGTATTGCCGGAAGCGTGGc                                                             <  1:733806/84‑1 (MQ=255)                                                                                                                            tGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGAGGTACGAGTATTGCCGGAAGCGTGGc                                                             >  2:733806/1‑84 (MQ=255)                                                                                                                                aGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGAGGTACGAGTATTGCCGGAAGCGTGGCCTGTATCCGGATGCAGAGTCTTATCCGTGGAAATCGAACGCGCATTACTGGTTGGTTAc  <  2:118712/139‑1 (MQ=255)                                                                                                                                aGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGAGGTACGAGTATTGCCGGAAGCGTGGCCTGTATCCGGATGCAGAGTCTTATCCGTGGAAATCGAACGCGCATTACTGGTTGGTTAc  <  1:129736/139‑1 (MQ=255)                                                                                                                                      |                                                                                                                                     TGTACTTTTCATTCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGAGGTACGAGTATTGCCGGAAGCGTGGCCTGTATCCGGATGCAGAGTCTTATCCGTGGAAATCGAACGCGCATTACTGGTTGGTTAC  >  NC_000913/566193‑566458

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑