Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913566,2450GA36.4% 29.0 / 29.1 33pseudogene (132/279 nt)exoDpseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related
Reads supporting (aligned to +/- strand):  ref base G (11/10);  new base A (3/9);  total (14/19)
Fisher's exact test for biased strand distribution p-value = 1.60e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.71e-01
Rejected as consensus: Frequency below/above cutoff threshold.

TGCTCCCCAAATACAAAACCAATTTCAGCCAGTGCCTCGTCCATTTTTTCGATGAACTCCGGCACCATCTCGTCAAAACTCGCCATGTACTTTTCATTCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGAGGTACGA  >  NC_000913/566108‑566380
                                                                                                                                         |                                                                                                                                       
tGCTCCCCAAATACAAAACCAATTTCAGCCAGTGCCTCGTCCATTTTTTCGATGAACTCCGGCACCATCTCGTCAAAACTCGCCATGTACTTTTCATTCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATgc                                                                                                                                        <  1:177161/139‑1 (MQ=255)
 gCTCCCCAAATACAAAACCAATTTCAGCCAGTGCCTCGTCCATTTTTTCGATGAACTCCGGCACCATCTCGTCAAAACTCGCCATGTACTTTTCATTCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATgcg                                                                                                                                       <  1:601410/139‑1 (MQ=255)
     cccAAATACAAAACCAATTTCAGCCAGTGCCTCGTCCATTTTTTCGATGAACTCCGGCACCATCTCGTCAAAACTCGCCATGTACTTTTCATTCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCggg                                                                                                                                   <  2:482223/139‑1 (MQ=255)
     cccAAATACAAAACCAACTTCAGCCAGTGCCTCGTCCATTTTTTCGATGAACTCCGGCACGCTCTCGTCAAAACTCGCCATGTACTTTTCATCCCGCCCAATCACGACATAATGCAGGCCTTCACGCTTCATACGCggt                                                                                                                                   <  1:481639/139‑2 (MQ=255)
            aCAAAACCAATTTCAGCCAGTGCCTCGTCCATTTTTTCGATGAACTCCGGCACCATTTCGTCAAAACTCGCCATGTACTTTTCATTCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGt                                                                                                                            <  2:71819/139‑1 (MQ=255)
                     aTTTCAGCCAGTGCCTCGTCCATTTTTTCGATGAACTCCGGCACCATCTCGTCAAAACTCGCCATGTACTTTTCATTCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGt                                                                                                                   >  1:104325/1‑139 (MQ=255)
                                        ccATTTTTTCGATGAACTCCGGCACGATCTCGTCAAAACTCGCCATGTACTTTTCATCCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGt                                                                                                <  1:424138/139‑1 (MQ=255)
                                             ttttCGATGAACTCCGGCACGATCTCGTCAAAACTCGCCATGTACTTTTCATCCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCAccc                                                                                           <  1:420253/139‑1 (MQ=255)
                                             ttttCGATGAACTCCGGCACCATCTCGTCAAAACTCGCCATGTACTTTTCATTCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCAccc                                                                                           <  1:138285/139‑1 (MQ=255)
                                              tttCGATGAACTCCGGCACGATCTCGTCAAAACTCGCCATGTACTTTTCATCCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCca                                                                                          <  2:442079/139‑1 (MQ=255)
                                               ttCGATGAACTCCGGCACCATCTCGTCAAAACTCGCCATGTACTTTTCATTCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCcac                                                                                         <  1:778745/139‑1 (MQ=255)
                                                              cACCATCTCGTCAAAACTCGCCATGTACTTTTCATTCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCAcc                                                                          <  1:221002/139‑1 (MQ=255)
                                                                  aTCTCGTCAAAACTCGCCATGTACTTTTCATTCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTggg                                                                      <  2:104325/139‑1 (MQ=255)
                                                                   tctcGTCAAAACTCGCCATGTACTTTTCATTCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATgcg                                                                                                                                       >  1:575116/1‑73 (MQ=255)
                                                                   tctcGTCAAAACTCGCCATGTACTTTTCATTCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATgcg                                                                                                                                       <  2:575116/73‑1 (MQ=255)
                                                                   tctcGTCAAAACTCGCCATGTACTTTTCATTCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGc                                                                     >  2:83888/1‑139 (MQ=255)
                                                                                     tGTACTTTTCATCCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCCGTACTGCACCTGGGCCATGTAAGCTGACTTTAt                                                   <  1:361636/139‑1 (MQ=255)
                                                                                                 tCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTc                                             <  1:307967/133‑1 (MQ=255)
                                                                                                 tCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTc                                             >  2:307967/1‑133 (MQ=255)
                                                                                                 cccGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCTGACTTTATGGCCTCGAAacc                                       >  1:200323/2‑139 (MQ=255)
                                                                                                    gCTCAATTACGCCATAATGCAGACCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCATTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTATGCCGATTTTATTGCATCGAAaccacc                                    >  2:395109/1‑139 (MQ=255)
                                                                                                    gCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTggg                                                                      >  1:286164/1‑105 (MQ=255)
                                                                                                    gCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTggg                                                                      <  2:286164/105‑1 (MQ=255)
                                                                                                           cACGACATAATGCAGGCCTTCACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCTGACTTTATGGCCTCGAAACCACCGAGCCgg                             <  2:230527/139‑1 (MQ=255)
                                                                                                                    aTGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATg                    <  2:331888/139‑1 (MQ=255)
                                                                                                                        aGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAAt                >  2:707390/1‑139 (MQ=255)
                                                                                                                          gCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATcc              >  2:89829/1‑139 (MQ=255)
                                                                                                                          gCCTTCACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGt                                                                                                <  2:256905/57‑1 (MQ=255)
                                                                                                                          gCCTTCACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGt                                                                                                >  1:256905/1‑57 (MQ=255)
                                                                                                                          gCCTTCACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTaa                                                              <  1:781703/91‑1 (MQ=255)
                                                                                                                          gCCTTCACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTaa                                                              >  2:781703/1‑91 (MQ=255)
                                                                                                                          gCCTTCACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCTGACTTTATGGCCTCGAAACCACCGAGCCGGAACTTCATGAAATcc              <  1:495817/139‑1 (MQ=255)
                                                                                                                               cACGCTTCATGCGCGGGTCTTAGTTGGCACAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCGGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGa         >  1:522595/1‑139 (MQ=255)
                                                                                                                               cACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATg                                                                                      <  1:609909/62‑1 (MQ=255)
                                                                                                                               cACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATg                                                                                      >  2:609909/1‑62 (MQ=255)
                                                                                                                                      cATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTGATGAAATCCCGGGAGGTACGa  >  1:459933/1‑139 (MQ=255)
                                                                                                                                      cATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGAGGTACGa  >  1:60149/1‑139 (MQ=255)
                                                                                                                                         |                                                                                                                                       
TGCTCCCCAAATACAAAACCAATTTCAGCCAGTGCCTCGTCCATTTTTTCGATGAACTCCGGCACCATCTCGTCAAAACTCGCCATGTACTTTTCATTCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGAGGTACGA  >  NC_000913/566108‑566380

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑