Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	566,277	0	C	T	35.9%	68.0 / 53.4	64	pseudogene (100/279 nt)	exoD	pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related
Reads supporting (aligned to +/- strand):  ref base C (18/23);  new base T (13/10);  total (31/33)
Fisher's exact test for biased strand distribution p-value = 4.36e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.54e-01
Rejected as consensus: Frequency below/above cutoff threshold.

CATTTTTTCGATGAACTCCGGCACCATCTCGTCAAAACTCGCCATGTACTTTTCATTCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGAGGTACGAGTATTGCCGGAAGCGTGGC  >  NC_000913/566149‑566399                                                                                                                                 |                                                                                                                           cATTTTTTCGATGAACTCCGGCACCATCTCGTCAAAACTCGCCATGTACTTTTCATTCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTc                                                                                                                  <  2:420904/139‑1 (MQ=255)          gATGAACTCCGGCACCATCTCGTCAAAACTCGCCATGTACTTTTCATTCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATg                                                                                                         <  1:180713/139‑1 (MQ=255)          gATGAACTCCGGCACCATCTCGTCAAAACTCGCCATGTACTTTTCATTCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATg                                                                                                         <  2:614853/139‑1 (MQ=255)          gATGAACTCCGGCACCATCTCGTCAAAACTCGCCATGTACTTTTCATTCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATg                                                                                                         <  1:41443/139‑1 (MQ=255)                cTCCGGCACGATCTCGTCAAAACTCGCCATGTACTTTTCATCCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTAc                                                                                                   <  1:344728/139‑1 (MQ=255)                     gCACCATCTCGTCAAAACTCGCCATGTACTTTTCGTTCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCAc                                                                                              <  2:741481/139‑1 (MQ=255)                         gaTCTCGTCAAAACTCGCCATGTACTTTTCATCCCGCTCAATCACGACATAATGCAGGCCTTCACGATTCATACGCGGGTCATAGTTGGCAAAGTACCCGGCATTTTTTCGCGTGACCCACATGGTGTACTACACCTgg                                                                                          <  1:511869/138‑1 (MQ=255)                          aTCTCGTCAAAACTCGCCATGTACTTTTCATTCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTggg                                                                                         >  1:597268/1‑139 (MQ=255)                           tctcGTCAAAACTCGCCATGTACTTTTCATCCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGc                                                                                        >  1:526432/1‑139 (MQ=255)                                         gCCATGTACTTTTCATTCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCcaca                                                                                                           <  1:112927/106‑1 (MQ=255)                                         gCCATGTACTTTTCATTCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCcaca                                                                                                           >  2:112927/1‑106 (MQ=255)                                         gCCATGTACTTTTCATTCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCt                                                                                                       <  2:347090/110‑1 (MQ=255)                                         gCCATGTACTTTTCATTCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCt                                                                                                       >  1:347090/1‑110 (MQ=255)                                                    ttCATTCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATg                                                                                                         <  2:175116/97‑1 (MQ=255)                                                    ttCATTCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATg                                                                                                         >  1:175116/1‑97 (MQ=255)                                                         tCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTa                                                                       >  2:160240/1‑126 (MQ=255)                                                         tCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTa                                                                       <  1:160240/126‑1 (MQ=255)                                                         cccGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTcg                                                                                                                      >  1:434711/2‑79 (MQ=255)                                                         cccGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTcg                                                                                                                      <  2:434711/78‑1 (MQ=255)                                                         cccGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAg                                                                                >  1:243370/2‑117 (MQ=255)                                                         cccGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAg                                                                                <  2:243370/116‑1 (MQ=255)                                                            gCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCt                                                                 <  1:11407/129‑1 (MQ=255)                                                            gCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCt                                                                 >  2:11407/1‑129 (MQ=255)                                                            gCTCAATCACGACATAATGCAGGCCTTCACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATg                                                                                                         >  1:340869/1‑89 (MQ=255)                                                            gCTCAATCACGACATAATGCAGGCCTTCACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATg                                                                                                         <  2:340869/89‑1 (MQ=255)                                                             cTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCg                                                      >  2:691249/1‑139 (MQ=255)                                                                           aaTGCAGGCCTTCACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCAccc                                                                                                              <  2:654029/69‑1 (MQ=255)                                                                           aaTGCAGGCCTTCACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCAccc                                                                                                              >  1:654029/1‑69 (MQ=255)                                                                                aGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCAccc                                                                                                              <  2:40775/64‑1 (MQ=255)                                                                                aGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCAccc                                                                                                              >  1:40775/1‑64 (MQ=255)                                                                                  gCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCcac                                                                                                            <  2:801591/64‑1 (MQ=255)                                                                                  gCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCcac                                                                                                            >  1:801591/1‑64 (MQ=255)                                                                                  gCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAAt                                   <  1:670644/137‑1 (MQ=255)                                                                                  gCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAAt                                   <  1:709391/137‑1 (MQ=255)                                                                                  gCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAAt                                   >  2:670644/1‑137 (MQ=255)                                                                                  gCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAAt                                   >  2:709391/1‑137 (MQ=255)                                                                                   ccTTCACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCTGACTTTATGGCCTCGAAACCACCGAGCCGGAACTTCATGAAATccc                                >  1:733003/1‑139 (MQ=255)                                                                                     ttCACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGt                                                                                                                   <  2:834763/54‑1 (MQ=255)                                                                                     ttCACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGt                                                                                                                   >  1:834763/1‑54 (MQ=255)                                                                                     ttCACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCTGACTTTAtggc                                                                   <  2:337505/102‑4 (MQ=255)                                                                                     ttCACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCTGACTTTAtggc                                                                   >  1:337505/1‑99 (MQ=255)                                                                                     tccACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTAGCGTCACCCACATGCTGTACTGCACCTGGGCCAAGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAAACGCgg                              >  2:290948/3‑139 (MQ=255)                                                                                      tCATGCTTCATGGGCGGCACATAGTGAGCAAAATACCAGACATCTTTTCGCGTCACCCACATACTGGACTGCTCCTGAGCCATGTAAGCCGATTTTATGGCCTCGAAACCACCGAACCGGAATTTCATTAAATCCCggg                             <  2:416753/139‑1 (MQ=255)                                                                                      tCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCggg                             <  1:691249/139‑1 (MQ=255)                                                                                      tCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCggg                             <  2:597268/139‑1 (MQ=255)                                                                                       cACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTACTGCACCTggg                                                                                         <  2:655084/78‑1 (MQ=255)                                                                                       cACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTACTGCACCTggg                                                                                         >  1:655084/1‑78 (MQ=255)                                                                                       cACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCTGACTTTATGGCCTCGAAACCACCGAGCCGGAACTTCATGAAATCCCGGGa                            >  1:564402/1‑139 (MQ=255)                                                                                       cACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCTGACTTTATGGCCTCGAAACCACCGAGCCGGAACTTCATGAAATCCCGGGa                            >  1:57386/1‑139 (MQ=255)                                                                                            ttCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATg                                                                                                         <  1:595647/57‑1 (MQ=255)                                                                                            ttCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATg                                                                                                         >  2:595647/1‑57 (MQ=255)                                                                                                tGCGCGGGTCATAGTTGGCAAAGTACCAGCCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCCCCGAGCCGGAATTTCCTGAAATCCCGGGAGGAACGaat                   >  1:416753/1‑137 (MQ=255)                                                                                                 gcgcGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGt                                                                                                                   <  2:419658/42‑1 (MQ=255)                                                                                                 gcgcGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGt                                                                                                                   >  1:419658/1‑42 (MQ=255)                                                                                                      ggTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCTGACTTTATGGCCTCGAAACCACCGAGCCGGAACTTCATGAAATCCCGGGAGGTaaacgggcattt             >  2:603920/1‑128 (MQ=255)                                                                                                      ggTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCcaca                                                                                                           >  1:131191/1‑45 (MQ=255)                                                                                                      ggTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCcaca                                                                                                           <  2:131191/45‑1 (MQ=255)                                                                                                      ggTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGAGGTACGAGTATTGcc             >  1:294959/1‑139 (MQ=255)                                                                                                        tCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATg                                                                                                         <  1:568378/45‑1 (MQ=255)                                                                                                        tCATAGTTGGCAAAGTACCAGGCAATTTTTCGCGTCACCCACATg                                                                                                         >  2:568378/1‑45 (MQ=255)                                                                                                          aTAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTAc                                                                                                   <  1:141678/49‑1 (MQ=255)                                                                                                          aTAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTAc                                                                                                   >  2:141678/1‑49 (MQ=255)                                                                                                                 gCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGAGGTACGAGTATTGCCGGAAGCGTGGc  <  2:365305/139‑1 (MQ=255)                                                                                                                 ccAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGAGGTACGAGTATTGCCGGAAGCGTGGc  <  2:393754/138‑1 (MQ=255)                                                                                                                                 |                                                                                                                           CATTTTTTCGATGAACTCCGGCACCATCTCGTCAAAACTCGCCATGTACTTTTCATTCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGAGGTACGAGTATTGCCGGAAGCGTGGC  >  NC_000913/566149‑566399

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑