Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913566,2770CT46.8% 10.0 / 62.3 47pseudogene (100/279 nt)exoDpseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related
Reads supporting (aligned to +/- strand):  ref base C (14/11);  new base T (10/12);  total (24/23)
Fisher's exact test for biased strand distribution p-value = 5.64e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.15e-02
Rejected as consensus: Frequency below/above cutoff threshold.

CCATTTTTTCGATGAACTCCGGCACCATCTCGTCAAAACTCGCCATGTACTTTTCATTCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGAGGTACGAGTATTGCCGGAAGCGTGGCCTGTATCCG  >  NC_000913/566148‑566408
                                                                                                                                 |                                                                                                                                   
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)
                           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                                                                                                                            >  1:256905/1‑57 (MQ=255)
                                                                                  gCCTTCACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGt                                                                                                                            <  2:256905/57‑1 (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                                                                                                                  >  2:609909/1‑62 (MQ=255)
                                                                                       cACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATg                                                                                                                  <  1:609909/62‑1 (MQ=255)
                                                                                              cATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTGATGAAATCCCGGGAGGTACGa                              >  1:459933/1‑139 (MQ=255)
                                                                                              cATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGAGGTACGa                              >  1:60149/1‑139 (MQ=255)
                                                                                               atacgcgGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCTGACTTTATGGCCTCGAAACCACCGAGCCGGAACTTCATGAAATCCCGGGAGGTaaacg                             >  2:674857/4‑135 (MQ=255)
                                                                                                tacgcgGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCTGACTTTATGGCCTCGAAACCACCGAGCCGGAACTTCATGAAATCCCGGGAGGTaaacgg                            >  2:700623/3‑134 (MQ=255)
                                                                                                      ggTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTAc                                                                                                            <  1:229203/53‑1 (MQ=255)
                                                                                                      ggTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTAc                                                                                                            >  2:229203/1‑53 (MQ=255)
                                                                                                      ggTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCTGACTTTATGGCCTCGAAACCACCGAGCCGGAACTTCATGAAATCCCGGGAGGTaaacgggcattt                      >  1:596155/1‑128 (MQ=255)
                                                                                                      ggTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCTGACTTTATGGCCTCGAAACCACCGAGCCGGAACTTCATGAAATCCCGGGAGGTaaacgggcattt                      >  2:430858/1‑128 (MQ=255)
                                                                                                      ggTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCTGACTTTATGGCCTCGAAACCACCGAGCCGGAACTTCATGAAATCCCGGGAGGTaaacgggcattt                      <  2:143571/139‑12 (MQ=255)
                                                                                                      ggTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGAGGTACGAGTATTGcc                      >  2:629094/1‑139 (MQ=255)
                                                                                                       gTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGAGGTACGAGTATTGCCg                     <  1:83888/139‑1 (MQ=255)
                                                                                                           tAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCTGACTTTATGGCCTCGAAACCACCGAGCCGGAACTTCATGAAATCCCg                                        <  1:407553/116‑1 (MQ=255)
                                                                                                           tAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCTGACTTTATGGCCTCGAAACCACCGAGCCGGAACTTCATGAAATCCCg                                        >  2:407553/1‑116 (MQ=255)
                                                                                                                 gCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTAc                                                                                                            >  2:318547/1‑42 (MQ=255)
                                                                                                                 gCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTAc                                                                                                            <  1:318547/42‑1 (MQ=255)
                                                                                                                 gCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGAGGTACGAGTATTGCCGGAAGCGTGGc           >  2:22031/1‑139 (MQ=255)
                                                                                                                 gCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGAGGTACGAGTATTGCCGGAAGCGTGGc           >  1:661931/1‑139 (MQ=255)
                                                                                                                   aaaGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTACTGCAcc                                                                                                      >  1:754854/1‑46 (MQ=255)
                                                                                                                   aaaGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTACTGCAcc                                                                                                      <  2:754854/46‑1 (MQ=255)
                                                                                                                          cAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGAGGTACGAGTATTGCCGGAAGCGTGGCCTGTATCCg  <  2:165117/139‑1 (MQ=255)
                                                                                                                                 cTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGt                                                                                            >  2:199684/1‑42 (MQ=255)
                                                                                                                                 cTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGt                                                                                            <  1:199684/42‑1 (MQ=255)
                                                                                                                                 |                                                                                                                                   
CCATTTTTTCGATGAACTCCGGCACCATCTCGTCAAAACTCGCCATGTACTTTTCATTCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGGAGGTACGAGTATTGCCGGAAGCGTGGCCTGTATCCG  >  NC_000913/566148‑566408

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑